diff --git a/CHANGELOG.md b/CHANGELOG.md
index 96a3427..29220e0 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,22 @@ Each release's binaries and full notes are on the
 [releases page](https://github.com/DylanCosto/bonefish/releases). "Output" means the alignment
 records. Each entry quotes the MD5 of the genome-wide HG001 sample's SAM output, `@PG` lines removed.
 
+## v0.3.0 (unreleased)
+
+**New: `-x tx`.** The preset maps direct RNA or cDNA to a transcriptome for quantifiers such as
+oarfish and NanoCount (minimap2 `-ax map-ont -N 100`).
+
+- **Speed:** on HG002 it is 2.3x (cDNA) and 2.8x (direct RNA) faster than minimap2.
+- **Accuracy:** it maps the same reads as minimap2. oarfish gene counts agree at r = 0.9995 or
+  higher. Report: `docs/validation/2026-10-21-transcriptome/`.
+
+**Faster with many reference sequences:** the ALT-contig count is computed once per index, not
+by scanning every target for every read. This matters for transcriptomes and metagenome
+assemblies.
+
+**Faster chaining:** isolated anchors are dropped before chaining. DNA uses 1.2% less CPU, with
+output unchanged (`9bc7ff3e…`).
+
 ## v0.2.0 (2026-10-21)
 
 **New: direct RNA and cDNA.** Spliced alignment to a genome is available through two presets:
diff --git a/README.md b/README.md
index 64fb8d2..18f5107 100644
--- a/README.md
+++ b/README.md
@@ -6,7 +6,8 @@ RNA and cDNA reads to a reference genome. It writes SAM, PAF or a sorted, indexe
 - **Accurate.** On whole human genomes (GIAB HG002 and HG005), SNP, indel and structural-variant
   calls match minimap2's. Methylation calls agree at r = 0.999.
 - **Fast.**
-  - Aligner alone: 2.6-8x faster than minimap2 on DNA, 2.6x on direct RNA and 5.4x on cDNA.
+  - Aligner alone: 2.6-8x faster than minimap2 on DNA, 2.6x on direct RNA, 5.4x on cDNA and
+    2.3-2.8x for transcriptome quantification.
   - Reads to a sorted BAM: about 3x faster than `minimap2 | samtools sort`.
 - **Drop-in.** It reads dorado's BAM output, keeping methylation and other tags, and accepts
   minimap2's options and preset names.
@@ -53,6 +54,7 @@ in a few minutes.
 | `dna` (default) | genomic DNA: R10.4.1 or R9.4.1, sup or hac, ultra-long (minimap2 `lr:hq`) |
 | `rna` | direct RNA (minimap2 `splice -uf -k14`) |
 | `cdna` | cDNA (minimap2 `splice`) |
+| `tx` | RNA or cDNA to a transcriptome, for quantification with oarfish or NanoCount (minimap2 `map-ont -N 100`) |
 
 Input formats, output options, memory use and CPU support are covered in
 [docs/usage.md](docs/usage.md). To replace minimap2 in an existing pipeline, including ONT's
@@ -81,9 +83,11 @@ Sniffles2 against GIAB v5.0q.
 | DNA, HG002 R9.4.1 chr20 (4.6 Gbp) | 412 s | 103 s | 4.0x |
 | cDNA, HG002 PCS114 (809k reads) | 1,223 s | 227 s | 5.4x |
 | direct RNA, HG002 RNA004 (902k reads) | 456 s | 177 s | 2.6x |
+| direct RNA to the transcriptome (`-x tx`, 200k reads) | 106 s | 37 s | 2.8x |
 
 On RNA, 99.5-99.9% of primary alignments are identical to minimap2's, and junction accuracy
-against GENCODE is the same.
+against GENCODE is the same. Transcript quantification from `-x tx` alignments agrees with
+minimap2's at gene level at r = 0.9995-0.99997.
 
 bonefish is also faster than dorado's aligner (4.3x), mm2plus (5.1x), mm2-fast (14x) and
 Winnowmap2 (38x).
diff --git a/bonefish-core/src/align/index.rs b/bonefish-core/src/align/index.rs
index 8dc61ba..9053ab4 100644
--- a/bonefish-core/src/align/index.rs
+++ b/bonefish-core/src/align/index.rs
@@ -135,6 +135,10 @@ pub struct Index {
     /// computed on first use for the ava self-skip fast path. See [`name_rank`].
     #[serde(skip)]
     name_rank: std::sync::OnceLock<NameRankData>,
+    /// Derived (not serialized): number of ALT contigs, counted on first use (after `--alt` has
+    /// marked them), so per-read code does not scan every target (500k+ for a transcriptome).
+    #[serde(skip)]
+    n_alt: std::sync::OnceLock<usize>,
 }
 
 /// Dense lexicographic ranking of target-sequence names, used to turn the
@@ -211,6 +215,7 @@ impl IndexBuilder {
                 backend: LookupBackend::BucketHash(super::index_bucket::BucketHashLookup::empty()),
                 packed_seqs: Default::default(),
                 name_rank: Default::default(),
+                n_alt: Default::default(),
             },
             w, k, max_occ,
             bucket_bits,
@@ -304,6 +309,11 @@ impl IndexBuilder {
 }
 
 impl Index {
+    /// Number of ALT contigs (computed once).
+    pub fn n_alt(&self) -> usize {
+        *self.n_alt.get_or_init(|| self.seqs.iter().filter(|s| s.is_alt).count())
+    }
+
     /// Dense lexicographic ranking of the target names, computed once on first use and cached
     pub fn name_rank(&self) -> &NameRankData {
         self.name_rank.get_or_init(|| {
@@ -538,6 +548,7 @@ impl Index {
                 backend: LookupBackend::BucketHash(lookup),
                 packed_seqs: Storage::mapped(map.clone(), qo, qn),
                 name_rank: Default::default(),
+                n_alt: Default::default(),
             });
             pos += hdr.part_len;
             pos += pad_to(pos, RAW_ALIGN);
@@ -707,6 +718,7 @@ impl Index {
             backend,
             packed_seqs: packed_seqs.into(),
             name_rank: Default::default(),
+            n_alt: Default::default(),
         };
 
         eprintln!("[*] Index loaded: {} seqs, {}M bases in {:.1}s",
@@ -727,6 +739,7 @@ impl Index {
             backend: LookupBackend::BucketHash(super::index_bucket::BucketHashLookup::empty()),
             packed_seqs: Default::default(),
             name_rank: Default::default(),
+            n_alt: Default::default(),
         }
     }
 
@@ -740,6 +753,7 @@ impl Index {
             backend: LookupBackend::BucketHash(super::index_bucket::BucketHashLookup::empty()),
             packed_seqs: Default::default(),
             name_rank: Default::default(),
+            n_alt: Default::default(),
         }
     }
 
@@ -769,6 +783,7 @@ impl Index {
             backend: LookupBackend::BucketHash(super::index_bucket::BucketHashLookup::empty()),
             packed_seqs: Default::default(),
             name_rank: Default::default(),
+            n_alt: Default::default(),
         };
 
         let mut offset = 0usize;
diff --git a/bonefish-core/src/align/map.rs b/bonefish-core/src/align/map.rs
index b861294..7aff37b 100644
--- a/bonefish-core/src/align/map.rs
+++ b/bonefish-core/src/align/map.rs
@@ -652,6 +652,36 @@ fn get_minimizer_index(qlen: usize, a: &Minimizer, mini_pos: &[u64]) -> Option<u
 }
 
 /// Estimate chain divergence from minimizer matching
+/// Remove anchors (sorted by `x`) with no other anchor of the same reference and strand within
+/// `max_dist` reference bases. Such an anchor is outside every other anchor's chaining window,
+/// so it can only form a one-anchor chain, which `min_cnt` (> 1) always drops: the chains are
+/// the same without it. A transcriptome yields many such scattered hits (a k-mer of the read
+/// on hundreds of short transcripts).
+fn drop_isolated_anchors(a: &mut Vec<Minimizer>, max_dist: i32, min_cnt: i32) {
+    let n = a.len();
+    if min_cnt <= 1 || n < 2 {
+        return;
+    }
+    let md = max_dist.max(0) as u64;
+    let near = |p: &Minimizer, q: &Minimizer| p.x >> 32 == q.x >> 32 && q.x.wrapping_sub(p.x) <= md;
+    let mut w = 0;
+    for i in 0..n {
+        if (i > 0 && near(&a[i - 1], &a[i])) || (i + 1 < n && near(&a[i], &a[i + 1])) {
+            a[w] = a[i];
+            w += 1;
+        }
+    }
+    a.truncate(w);
+}
+
+/// Copy each region's chain anchors (`anchor_count` from offset `original_as` of `chains`).
+fn fill_anchors(regs: &mut [Mapping], chains: &[Minimizer]) {
+    for r in regs.iter_mut() {
+        let (a, n) = (r.original_as, r.anchor_count as usize);
+        r.anchors = chains[a..a + n].to_vec();
+    }
+}
+
 fn estimate_divergence(regs: &mut [Mapping], _anchors: &[Minimizer], qlen: usize, mini_pos: &[u64], mi: &Index) {
     if mini_pos.is_empty() { return; }
 
@@ -839,6 +869,13 @@ pub fn map_query(
     // presets), otherwise DP
     let is_splice = opt.flags.contains(AlignFlags::SPLICE);
     let mut anchors = std::mem::take(&mut ctx.anchors);
+    // The rescue's density test below counts every anchor, isolated ones included.
+    let n_anchors = anchors.len();
+    if !is_splice && !opt.flags.intersects(AlignFlags::RMQ_CHAIN | AlignFlags::PAR_CHAIN) {
+        // Widest reference distance any chaining pass of this read uses (main, the -g re-chain).
+        let reach = opt.chaining.max_gap.max(max_chain_gap_ref).max(opt.chaining.bandwidth);
+        drop_isolated_anchors(&mut anchors, reach, opt.chaining.min_cnt);
+    }
     let (mut u, mut chains) = if is_splice {
         chain_anchors_cdna(&opt.chaining, max_chain_gap_ref, max_chain_gap_qry, &mut anchors, &mut ctx.chain_bufs)
     } else if opt.flags.contains(AlignFlags::RMQ_CHAIN) {
@@ -889,7 +926,7 @@ pub fn map_query(
             let needs_rescue = ((qlen.saturating_sub(coverage) > opt.chaining.rmq_rescue_size as usize)
                 || (coverage > (qlen as f32 * opt.chaining.rmq_rescue_ratio) as usize))
                 && crate::align::env_flags::EXP_RESCUE_COVER.is_none_or(|f| (coverage as f32) < f * qlen as f32)
-                && (opt.chaining.rescue_max_density == 0 || ctx.anchors.len() < opt.chaining.rescue_max_density as usize * qlen);
+                && (opt.chaining.rescue_max_density == 0 || n_anchors < opt.chaining.rescue_max_density as usize * qlen);
             let needs_rescue = needs_rescue && (!(opt.chaining.rescue_join || *crate::align::env_flags::EXP_RESCUE_JOIN) || {
                 let max_dist = opt.chaining.max_gap.max(opt.chaining.bandwidth_long);
                 let j = chains_joinable(&u, &chains, max_dist, opt.chaining.bandwidth_long);
@@ -952,12 +989,12 @@ pub fn map_query(
 
         if cnt == 0 { continue; }
 
-        // Collect chain anchors
-        let chain_anchors_vec = chains[k_offset..k_offset + cnt as usize].to_vec();
-
+        // The chain's anchors are copied into the region only if it survives the parent /
+        // secondary filtering below (`fill_anchors`): with many overlapping chains per read
+        // (repeats, transcript isoforms) most regions are dropped there.
         let is_qstrand = opt.flags.contains(AlignFlags::QSTRAND);
         let ChainCoords { rid, rev, rs, re, qs, qe, hash: chain_hash } =
-            chain_coords(&chain_anchors_vec, qseq.len(), is_qstrand, read_hash);
+            chain_coords(&chains[k_offset..k_offset + cnt as usize], qseq.len(), is_qstrand, read_hash);
 
         regs.push(Mapping {
             ref_id: rid,
@@ -968,7 +1005,7 @@ pub fn map_query(
             score: sc,
             initial_chain_score: sc,  // initially same as score
             anchor_count: cnt,
-            anchors: chain_anchors_vec,
+            anchors: Vec::new(),
             is_reverse: rev,
             s2_score: None,
             is_secondary: false,
@@ -1004,7 +1041,7 @@ pub fn map_query(
     }
 
     // Mark ALT-contig chains; then sort chains by descending score.
-    let n_alt = mi.seqs.iter().filter(|s| s.is_alt).count();
+    let n_alt = mi.n_alt();
     if n_alt > 0 {
         for r in regs.iter_mut() {
             if mi.seqs[r.ref_id].is_alt { r.is_alt = true; }
@@ -1027,6 +1064,7 @@ pub fn map_query(
 
     // Skip parent-based filtering when ALL_CHAINS is set (e.g. ava-ont, ava-pb)
     if opt.flags.contains(AlignFlags::ALL_CHAINS) {
+        fill_anchors(&mut regs, &chains);
         // Nearby-seed computation on post-filter chains
         // Build squeezed anchor array from surviving chains, sorted by position
         let mut pos_order: Vec<usize> = (0..regs.len()).collect();
@@ -1219,6 +1257,7 @@ pub fn map_query(
         compacted.push(r);
     }
     regs = compacted;
+    fill_anchors(&mut regs, &chains);
     let mut filtered_regs = regs;
     let pc3 = Instant::now();
     PC_PARENT_NS.fetch_add((pc3 - pc2).as_nanos() as u64, Relaxed);
diff --git a/bonefish-core/src/align/pipeline.rs b/bonefish-core/src/align/pipeline.rs
index 53a4e99..4053ad5 100644
--- a/bonefish-core/src/align/pipeline.rs
+++ b/bonefish-core/src/align/pipeline.rs
@@ -1769,7 +1769,7 @@ fn process_query_core(
     let squeezed = map_result.squeezed;
     let split_mode = out.split_mode;
     // Mark ALT contigs on chains before sorting
-    let n_alt = mi.seqs.iter().filter(|s| s.is_alt).count();
+    let n_alt = mi.n_alt();
     if n_alt > 0 {
         for r in regs.iter_mut() {
             if mi.seqs[r.ref_id].is_alt { r.is_alt = true; }
diff --git a/bonefish-core/src/api.rs b/bonefish-core/src/api.rs
index 51c2788..36e287e 100644
--- a/bonefish-core/src/api.rs
+++ b/bonefish-core/src/api.rs
@@ -43,6 +43,8 @@ pub enum Preset {
     Cdna,
     /// Accurate cDNA, spliced (minimap2 `-x splice:hq`).
     SpliceHq,
+    /// RNA or cDNA reads to a transcriptome, for quantification (minimap2 `-x map-ont -N 100`).
+    Tx,
 }
 
 impl Preset {
@@ -53,6 +55,7 @@ impl Preset {
             Preset::Rna => "rna",
             Preset::Cdna => "cdna",
             Preset::SpliceHq => "splice:hq",
+            Preset::Tx => "tx",
         }
     }
 }
@@ -568,7 +571,7 @@ fn parse_cigar_string(s: &str) -> Vec<CigarOp> {
 // ---------------------------------------------------------------------------
 
 /// Apply a preset by string name ("dna" or one of its minimap2-name aliases, "rna", "cdna",
-/// "splice" (= cdna) or "splice:hq").
+/// "splice" (= cdna), "splice:hq" or "tx").
 ///
 /// This is the same function used by the CLI's `-x` flag. Modifies `opt`,
 /// `k` and `w` in place. Returns an error if the preset name
@@ -613,6 +616,18 @@ pub fn apply_preset_str(opt: &mut MapOptions, k: &mut usize, w: &mut usize, pres
             opt.alignment.gap_subanchor = true;
             opt.alignment.gap_subanchor_tr = 150;
         },
+        // Reads (direct RNA or cDNA) against a transcriptome, for quantifiers that take all
+        // alignments (oarfish, NanoCount, salmon): minimap2's map-ont seeding (k15 w10, no seed
+        // occurrence range, 5 kb query gap limit) for short and noisy RNA reads, up to 100
+        // secondary alignments per read (isoforms share most of their sequence), and otherwise
+        // the dna preset's cheaper chaining and DP (there are no introns to align).
+        "tx" => {
+            apply_preset_str(opt, k, w, "dna")?;
+            *k = 15; *w = 10;
+            opt.chaining.max_gap = 5000;
+            opt.seeding.min_mid_occ = 10; opt.seeding.max_mid_occ = 1_000_000;
+            opt.filtering.best_n = 100;
+        },
         // Spliced alignment of transcripts, as minimap2 2.30/2.31 `-x splice` (options.c): k15 w5,
         // both transcript strands tried (-ub) with splice-site flank scoring, introns up to 200 kb
         // (-G: chaining reference gap and bandwidth), cDNA-mode chaining, 2 kb query gap limit,
@@ -1088,7 +1103,7 @@ mod tests {
 
     #[test]
     fn test_preset_as_str_roundtrip() {
-        let presets = [Preset::Dna, Preset::Rna, Preset::Cdna, Preset::SpliceHq];
+        let presets = [Preset::Dna, Preset::Rna, Preset::Cdna, Preset::SpliceHq, Preset::Tx];
         for p in &presets {
             let s = p.as_str();
             assert!(!s.is_empty(), "preset {:?} should have a string form", p);
diff --git a/bonefish/src/main.rs b/bonefish/src/main.rs
index c70abb6..2685f99 100644
--- a/bonefish/src/main.rs
+++ b/bonefish/src/main.rs
@@ -52,11 +52,13 @@ struct AlignArgs {
     ///   rna              — direct RNA vs a reference genome (spliced; minimap2 -x splice -uf -k14)
     ///   cdna             — cDNA vs a reference genome (spliced; minimap2 -x splice); alias: splice
     ///   splice:hq        — accurate cDNA (minimap2 -x splice:hq)
+    ///   tx               — RNA/cDNA vs a transcriptome, for quantification (minimap2 -x map-ont -N 100)
     /// dna = minimap2 lr:hq seeding and scoring plus --ext-bw 200 --ext-adaptive 64 --ext-rescue
     /// --ext-probe 2000,1000 --gap-bw-margin 500 --gap-bw-narrow 32 --ungapped-fill --max-gap-ref 5000
     /// --seg-rmq --clean-dp --rescue-join --rescue-max-density 2 --gap-subanchor-tr 150
     /// cdna = -k15 -w5 -g2k -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200,100 -ub --junc-bonus 9
     /// --junc-pen 5 --splice-flank yes; rna = cdna with -k14 -uf
+    /// tx = dna with -k15 -w10 -g5000 -U10,1000000 -N100
     #[arg(short = 'x', long, verbatim_doc_comment)]
     pub preset: Option<String>,
 
diff --git a/bonefish/tests/data/expected.tsv b/bonefish/tests/data/expected.tsv
index ee570ea..0cd2ec6 100644
--- a/bonefish/tests/data/expected.tsv
+++ b/bonefish/tests/data/expected.tsv
@@ -14,3 +14,4 @@ cdna_paf_cs	bonefish	-x cdna -c --cs	21afca13cdff0b35
 cdna_junc_bed	bonefish	-x cdna -a --junc-bed {junc}	6292d532a2fcabc3
 cdna_splice_hq	bonefish	-x splice:hq -a	1988a08a9ab7353a
 cdna_alias_splice	bonefish	-x splice -a	60d6d8c7c31cd299
+tx_sam	bonefish	-x tx -a	d53bfcfb58fa2138
diff --git a/bonefish/tests/regression.rs b/bonefish/tests/regression.rs
index 7220c5a..379d002 100644
--- a/bonefish/tests/regression.rs
+++ b/bonefish/tests/regression.rs
@@ -55,7 +55,8 @@ fn expected() -> Vec<(String, String, String, String)> {
 }
 
 /// Arguments for an expected.tsv case: its options (`{junc}` stands for the annotation BED), then
-/// the reference and reads. Cases named `rna_*` / `cdna_*` use the spliced dataset (made by
+/// the reference and reads (`tx_*` runs the transcriptome preset on the DNA dataset, for its
+/// seeding and secondary settings). Cases named `rna_*` / `cdna_*` use the spliced dataset (made by
 /// `scripts/make_regression_rna_data.py`): direct-RNA-like or cDNA-like reads on a genome of
 /// multi-exon genes.
 fn map_args(name: &str, case_args: &str) -> Vec<String> {
diff --git a/docs/benchmarks.md b/docs/benchmarks.md
index 221b269..6046b2f 100644
--- a/docs/benchmarks.md
+++ b/docs/benchmarks.md
@@ -96,6 +96,20 @@ the reference near the chain's anchors with a 10-mer search for unanchored exons
 aligned once for both transcript strands. Details:
 [validation/2026-10-21-rna-cdna](validation/2026-10-21-rna-cdna/README.md).
 
+## Transcriptome quantification
+
+`-x tx` against minimap2 `-ax map-ont -N 100` on GENCODE v49 transcripts (HG002, 200k reads each):
+
+| | minimap2 | bonefish `-x tx` |
+|---|---:|---:|
+| cDNA, wall | 185 s | 81 s |
+| direct RNA, wall | 106 s | 37 s |
+| reads mapped | | the same as minimap2 |
+| oarfish gene counts vs minimap2's: Pearson r | | 0.9995 (cDNA), 0.99997 (direct RNA) |
+
+On simulated reads, the primary lands on the true transcript at least as often as with minimap2.
+Details: [validation/2026-10-21-transcriptome](validation/2026-10-21-transcriptome/README.md).
+
 ## Metagenomes, duplex reads and rDNA
 
 Against minimap2 `lr:hq` on the same reads (v0.1.7): ONT's Zymo fecal reference (1.70 M R10.4.1 sup
diff --git a/docs/pipelines.md b/docs/pipelines.md
index 1b1d221..6538170 100644
--- a/docs/pipelines.md
+++ b/docs/pipelines.md
@@ -16,6 +16,7 @@ minimap2 in a pipeline in two ways:
 | `minimap2 -ax splice -uf -k14 ref.fa drna.fq` | `bonefish -x rna -a ref.fa drna.fq` |
 | `minimap2 -ax splice ref.fa cdna.fq` | `bonefish -x cdna -a ref.fa cdna.fq` |
 | `minimap2 -ax splice --junc-bed anno.bed ...` | `bonefish -x cdna -a --junc-bed anno.bed ...` |
+| `minimap2 -ax map-ont -N 100 transcripts.fa reads.fq` (for quantification) | `bonefish -x tx -a transcripts.fa reads.fq` |
 
 Notes:
 
@@ -75,6 +76,22 @@ minimap2 does.
 reads ([report](validation/2026-10-21-rna-cdna/README.md)), but not yet against these downstream
 tools.
 
+## Transcript quantification
+
+oarfish, NanoCount and similar quantifiers take reads aligned to the transcriptome with many
+secondary alignments. `-x tx` writes up to 100 secondaries per read, as `minimap2 -N 100` does:
+
+```bash
+bonefish -t 16 -x tx -a --eqx transcripts.fa reads.fq | samtools view -b -o tx.bam -
+```
+
+- **Agreement with minimap2:** on HG002 direct RNA and cDNA, oarfish gene counts from these
+  alignments agree with counts from minimap2's at r = 0.9995-0.99997. Simulated reads land on
+  their true transcript at least as often as with minimap2
+  ([report](validation/2026-10-21-transcriptome/README.md)).
+- **oarfish needs a workaround for now:** it only accepts BAMs whose `@PG` header names an
+  aligner it has validated, and bonefish is not yet on its list.
+
 ## Containers
 
 ```bash
diff --git a/docs/usage.md b/docs/usage.md
index 16920f6..b295f09 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -8,6 +8,7 @@
 | `rna` | direct RNA (RNA004), spliced to a genome | `-x splice -uf -k14` |
 | `cdna` | cDNA, spliced to a genome, transcript strand from splice signals | `-x splice` |
 | `splice:hq` | accurate cDNA | `-x splice:hq` |
+| `tx` | direct RNA or cDNA to a transcriptome, for quantification (oarfish, NanoCount) | `-x map-ont -N 100` |
 
 The minimap2 names `lr:hq`, `lr:hq-fast`, `map-ont` and `lr` are accepted for `dna`, and `splice`
 for `cdna`. PacBio, short-read and assembly presets are not supported.
@@ -21,6 +22,7 @@ build an index once:
 bonefish -d ref.raw --idx-raw ref.fa              # dna; loads in under a second (8.5 GB for GRCh38)
 bonefish -x cdna -d cdna.raw --idx-raw ref.fa     # spliced presets need their own index (k/w differ)
 bonefish -x rna  -d rna.raw  --idx-raw ref.fa
+bonefish -x tx   -d tx.raw   --idx-raw transcripts.fa
 ```
 
 Without `--idx-raw`, `-d` writes a smaller index that takes a few seconds to load. Indexes are
diff --git a/docs/validation/2026-10-21-transcriptome/README.md b/docs/validation/2026-10-21-transcriptome/README.md
new file mode 100644
index 0000000..01cc28b
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/README.md
@@ -0,0 +1,90 @@
+# Transcriptome mapping for quantification (21 Oct 2026)
+
+Long-read quantifiers such as oarfish and NanoCount take reads aligned to a transcriptome, with
+many secondary alignments per read. Their usual input is `minimap2 -ax map-ont -N 100`. This
+report adds the `-x tx` preset for that workflow, and compares it with minimap2 and with
+bonefish's `dna` preset.
+
+## Data and method
+
+- **Reads:** the first 200,000 HG002 direct-RNA (RNA004 sup) and cDNA (PCS114 hac) reads of the
+  [RNA report](../2026-10-21-rna-cdna/README.md).
+- **Simulated reads:** Badread reads from 30,000 GENCODE transcripts, cDNA-like and
+  direct-RNA-like. Each read's source transcript and gene are known.
+- **Reference:** GENCODE v49 transcripts, 533,740 sequences
+  (`gencode.v49.transcripts.fa.gz`, sha256 `08ee7ee8…`).
+- **Commands:**
+  - minimap2 2.31: `-ax map-ont -N 100 --eqx`.
+  - bonefish: `-a --eqx`, with either `-x tx` or `-N 100` on the `dna` preset.
+  - Quantification: oarfish 0.10.3 with `--filter-group nanocount-filters`, compared with
+    `tx_quant_compare.py`.
+- **Machine:** Core i5-12600K, 16 threads.
+
+**oarfish and bonefish BAMs:** oarfish only reads BAMs whose `@PG` header names an aligner it
+has validated (minimap2, pbmm2, bramble or rammap). bonefish's BAMs were relabelled as rammap,
+bonefish's upstream, for this test. oarfish otherwise only needs the standard `AS` tag.
+
+## The `tx` preset
+
+- **Seeding:** minimap2's `map-ont` seeding. k=15 and w=10, with no occurrence range and a 5 kb
+  query gap limit, suit short, noisy RNA reads.
+- **Secondary alignments:** up to 100 per read (`-N 100`).
+- **Everything else:** the `dna` preset's chaining and DP. There are no introns in transcriptome
+  mapping, so they apply unchanged.
+
+## Results
+
+| 200k reads | minimap2 `map-ont -N 100` | bonefish `dna -N 100` | **bonefish `-x tx`** |
+|---|---:|---:|---:|
+| cDNA: wall / CPU-s | 185 s / 2,285 | 146 s / 1,535 | **81 s / 1,149** |
+| direct RNA: wall / CPU-s | 106 s / 1,026 | 102 s / 1,032 | **37 s / 485** |
+| unmapped reads (cDNA / direct RNA) | 1,987 / 37,838 | 2,493 / 39,115 | **1,987 / 37,838** |
+| oarfish genes vs minimap2: Pearson (cDNA / direct RNA) | | 0.99937 / 0.99968 | 0.99950 / 0.99997 |
+| reads assigned to another gene (cDNA / direct RNA) | | 0.65% / 0.55% | 0.66% / 0.25% |
+| reads assigned to another transcript (cDNA / direct RNA) | | 1.63% / 1.27% | 1.74% / 0.93% |
+| simulated cDNA: primary on true transcript / gene | 93.73% / 99.53% | 93.89% / 99.48% | 93.88% / 99.53% |
+| simulated direct RNA: mapped | 99.69% | 98.82% | 99.69% |
+| simulated direct RNA: primary on true transcript / gene | 91.98% / 99.33% | 91.33% / 98.49% | 92.17% / 99.34% |
+| simulated: true transcript among alignments (cDNA / direct RNA) | 99.89% / 99.68% | 99.85% / 98.80% | 99.89% / 99.68% |
+
+- **Sensitivity:** `-x tx` leaves exactly the same number of reads unmapped as minimap2. The `dna`
+  preset's sparser k=19 seeds missed some short reads.
+- **Accuracy:** on simulated reads, `-x tx` puts at least as many primaries on the true
+  transcript as minimap2. The true transcript is among the alignments as often.
+- **Quantification:** at gene level, quantification from `-x tx` agrees with minimap2's at
+  r = 0.9995 (cDNA) and 0.99997 (direct RNA). Assignment between isoforms, which is close to a
+  tie for many reads, differs for 0.9-1.7% of reads.
+- **Speed:** `-x tx` is 2.3x (cDNA) and 2.8x (direct RNA) faster than minimap2 in wall time.
+
+## What made it fast
+
+The first `tx` build was no faster than minimap2 (`runs/tx1`: cDNA 184 s, direct RNA 102 s).
+Profiling found three things:
+
+1. **A per-read scan of every reference sequence.** The code counted ALT contigs by looking at
+   all 533,740 transcript names twice per read. That was 32 of 35 post-chain thread-seconds on
+   20k reads. On the 195-sequence human genome it cost nothing, so it had never shown up. The
+   count is now made once per index (`runs/tx3`: cDNA 85 s, direct RNA 39 s). Anything with many
+   reference sequences, such as metagenome assemblies, gains as well.
+2. **Isolated anchors.** A read's k-mers hit hundreds of short transcripts, and most hits have no
+   other hit on the same transcript. They are now dropped before chaining, because they can only
+   form one-anchor chains, which are always discarded. Output is identical. Chaining is 8%
+   faster here, and DNA uses 1.2% less CPU (`runs/tx4`).
+3. **Anchor copies.** Chain anchors are now copied only for regions that survive the secondary
+   filter. This made little difference on its own.
+
+For all three changes, output stayed identical: the DNA genome-wide sample has the same MD5
+(`9bc7ff3e…`), every golden-output test passes, and the transcriptome SAM is unchanged.
+
+## Files
+
+- `evidence/runs/<run>/`: GNU time, stderr, oarfish logs and metadata.
+  - `mm2`: minimap2.
+  - `dna_N100`: the `dna` preset with `-N 100`.
+  - `tx1`, `tx3`, `tx4`: the `tx` preset at each step above.
+- `evidence/ledger.tsv`: one line per run.
+- `evidence/scripts/`: `tx_bench.sh` (runs and scoring), `tx_quant_compare.py` (oarfish count
+  correlation) and `tx_sim_truth.py` (simulated-read truth).
+
+The simulated reads are those of the RNA report (`rna_sim_reads.sh`). `SHA256SUMS` covers
+`evidence/`. Local paths are replaced by `${BENCH}`, `${DATA}`, `${REPO}` and `${HOME}`.
diff --git a/docs/validation/2026-10-21-transcriptome/SHA256SUMS b/docs/validation/2026-10-21-transcriptome/SHA256SUMS
new file mode 100644
index 0000000..ec4b308
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/SHA256SUMS
@@ -0,0 +1,64 @@
+8025b129f3312ca17fe73a47a389f86649876e7f6fb1f42c2083200659764d51  evidence/ledger.tsv
+8a94c61bec8aa2a21241e7a79ccdfa97d9e3850769a6e19ccc64d5b0c5afae71  evidence/runs/dna_N100/cdna.err
+5384c3d8d1ec64e31df631b19d9792a0ae2a585e8ceeca07a548e2d380955ffc  evidence/runs/dna_N100/cdna.oarfish.log
+ae0c22b699d9b9b365e56343eae0764af4414ae3dee5260f7ba3afd7a40b28cd  evidence/runs/dna_N100/cdna.oarfish.meta_info.json
+aa686c327cfedea2aaea413c4a65acf04d9fb2078eaf607b3cb936d5f1f62d32  evidence/runs/dna_N100/cdna.time
+f1cfed86480665e547d31ade9d1addfee042214245ab1fea370ddc5029b7b90e  evidence/runs/dna_N100/drna.err
+52f70a53a0de4aba88a9f649a1662d57c2763f7f925d80b493283acbffb066e8  evidence/runs/dna_N100/drna.oarfish.log
+b304a3d889f7c44b94a1263e6ce0d53bee2cb867d58db265c0abecc1c213f882  evidence/runs/dna_N100/drna.oarfish.meta_info.json
+7a16c5aaf7641b7099b6d3b6233975e12ca63c3c4e0b109102533c86e405aaba  evidence/runs/dna_N100/drna.time
+676f00c2a86110d49b69573ce54199ed0b3636c32dce34294bdb6344bb3a9ca9  evidence/runs/dna_N100/sim_cdna.err
+6bcc8c7b54add0e7f260d17a0897e78180931a2677cf1a1930d877f3bd737401  evidence/runs/dna_N100/sim_cdna.time
+6ad4f3cc8f53a2c4544e966162687ffde34ee697b98f70a12459dbd8ca639895  evidence/runs/dna_N100/sim_drna.err
+f6f54b7110a7d4480cdaa3d368a4c24d7362b1c2eaf6cc3486dfc0e14a903a51  evidence/runs/dna_N100/sim_drna.time
+8675dedfa639986dc63a71106095a1d24572504a8b7ca769f28bfdf3ccd98df4  evidence/runs/mm2/cdna.err
+3e798946ee9e95db459bab6d17555d0e8a358870597c62a683357f06ab2fa27e  evidence/runs/mm2/cdna.oarfish.log
+c2b3f9683b91fd979bbd6ca433b32cbfe50977aa4d3a8c3d2ddb65e328794622  evidence/runs/mm2/cdna.oarfish.meta_info.json
+01a9032811558cc0eb966bf812cafa2762b1b31964579e660f4152cd9777ff3a  evidence/runs/mm2/cdna.time
+db188083986318d5f4b11b3219bac3950f3c716b65792ce8caa9cff3d504e6ba  evidence/runs/mm2/drna.err
+7858d67f17738c43cf0eba5c58d2267247b848dcbc7aafd2b2224cff4ff68c06  evidence/runs/mm2/drna.oarfish.log
+5bc3693c0290a5be9d64a3c65f0db3d227797efec42ad6d49c327a6d00402dc6  evidence/runs/mm2/drna.oarfish.meta_info.json
+85795caf45eb55ab2f0fe50c51f40111a776c6726bd39d2fefed550e4864635f  evidence/runs/mm2/drna.time
+47062f5eeb8a9193e168c8f059776330566d7a78587541133c86a765f89beb1a  evidence/runs/mm2/sim_cdna.err
+846939527ce82e6ad1ba0a4828b12c67179ea19c93e10b792fe149959aa8bc22  evidence/runs/mm2/sim_cdna.time
+d6ac3015dd0700bd6ff346e2b03d27437528859be43777fd0c2bb80b0b30981b  evidence/runs/mm2/sim_drna.err
+a21746be10b7ca2dec41bb0cf742856edad731c7aba4f039450e8055dc968947  evidence/runs/mm2/sim_drna.time
+0c2a673b9249a77a4cd6206f49131cfdb4720dbbd050cbc10024e033dae919c0  evidence/runs/tx1/cdna.err
+e4a40d6c6f2958cc6d615b10959adff5da5418f25419e9cde7638d26bfd594af  evidence/runs/tx1/cdna.oarfish.log
+0abc27adefbfe1988f65db2a601aecf467e93e0f137a61f46e03c9f8a106220c  evidence/runs/tx1/cdna.oarfish.meta_info.json
+57757b6946c5e7238648e6cd4c7372e94507ac849e3fdf0736fd0d86ccf8338b  evidence/runs/tx1/cdna.time
+016d1418e3ca4e5b1a4e24772034198ae9c2279aa135522919956b0583be00ab  evidence/runs/tx1/drna.err
+f42bffa9e81ee8673e6c00f3b3c46bc73c5cd85cd06242b97a8b2298d548a13c  evidence/runs/tx1/drna.oarfish.log
+5678688ca7d3e9fe6f0866ef6e3020d802f04f641d0f8e551f2652cb4ca08529  evidence/runs/tx1/drna.oarfish.meta_info.json
+d545df618cc857b71c90df996908a0600489e4b2ae8ceb32987a85577709a826  evidence/runs/tx1/drna.time
+1c01a286ea1b2ff8be5073795263cf3bf6d8d71cdc66a0e459288e4eb43821d8  evidence/runs/tx1/sim_cdna.err
+80b6879f8343c872430b0182968b8fb719bb2e3235f5915ed52ca685e3068717  evidence/runs/tx1/sim_cdna.time
+e3513a944b00257e10fc14b216b6bd4d239033018a0f570fec9e6abb0c15c2fa  evidence/runs/tx1/sim_drna.err
+38d7861805cd8427211aa9beb2f2b8d65f82df44643835e4bf0b5287ff2b6426  evidence/runs/tx1/sim_drna.time
+e85197f9778db876cb7bf4a09e0144da7e0d7236a9f6b75b84098245d9c7f5dc  evidence/runs/tx3/cdna.err
+907cc2de423def8d4dba987d743554eecd6afa2e752fb38d3b4bdbf47c1d4961  evidence/runs/tx3/cdna.oarfish.log
+e386672798db8c2eb8da0a21382105c354a52a07bf6d238c31982eb24153f52e  evidence/runs/tx3/cdna.oarfish.meta_info.json
+bb4eac6358534762ad0c4bc6a579a2c362f99ae430ba04175aa7a6137c6295af  evidence/runs/tx3/cdna.time
+f32a5330cc5daa7cfef5bfa46260f559dd43e8c387cac402c80e6b8fb2903225  evidence/runs/tx3/drna.err
+099e092bd89e45135914cf94d2f2dcf4402d9d61249293976a44a8b40bd408ef  evidence/runs/tx3/drna.oarfish.log
+da99369453402c7ecaf23cf8151d7bbfbbb6e4bf483094f3a3549893264e8a27  evidence/runs/tx3/drna.oarfish.meta_info.json
+7f28fd91c684f89bb2505db140be1107f439aa9f1984c7c22b592908906e35ff  evidence/runs/tx3/drna.time
+e411519b5c393bdacc7836f07ec08d3ff197f6803f01cc9ebaf1f774683bde68  evidence/runs/tx3/sim_cdna.err
+455e0bfcb702bcfbcfd6ab33d609224a1a874ab1b9a1da2fc1d7324b6cabb9ca  evidence/runs/tx3/sim_cdna.time
+e117c27468b832ad60501d166d1e524899f5929b466a5c7bbade4acd16c87da7  evidence/runs/tx3/sim_drna.err
+d3965e076553442935173a1c439c4e6f8a2c771adaef3c87a2b9550148f3527d  evidence/runs/tx3/sim_drna.time
+e1ebbd87d36b253f6d971ba227df5445d3f64a37aeda9bac1514344bef43bca2  evidence/runs/tx4/cdna.err
+832bf3c3a53c950ce756bc9179eb94d80268348efe858b14b36f3470a986bb80  evidence/runs/tx4/cdna.oarfish.log
+2034f3465326110e500bba277593d96f509ea5d876aada07df220214c0d5db48  evidence/runs/tx4/cdna.oarfish.meta_info.json
+c4fe07dd2af4f6ad627de8f16b0790caf8646fddc9681c2dfea3b4bce6dc0092  evidence/runs/tx4/cdna.time
+c9cee6c81876786f1989d410fe5af2d63d9035463a5b5ddbc3667c0e06084770  evidence/runs/tx4/drna.err
+e407175f2c3ab8f01978b7fc68684bb0fc029c978ea735da9071abebd6dba513  evidence/runs/tx4/drna.oarfish.log
+e384647a8d00e44c70d1435b7ebc290adb28f3cfe8b32253442c29aa889b8fbb  evidence/runs/tx4/drna.oarfish.meta_info.json
+68e7e11c61885ffb9fee25586c270191334b2819b4365c71af3b3c81591733e1  evidence/runs/tx4/drna.time
+055ba99e622ccf003d22d45a768ed0f2faa32610d005339b6ac7f0a23e2083ab  evidence/runs/tx4/sim_cdna.err
+6fcac4c9e963b42056521450866a9793d4f1573c5b7a88bc6e2d8db63f743f75  evidence/runs/tx4/sim_cdna.time
+46f044fbd53935795298e7403e71ce348c1289b05500998b4c3501ed12891c66  evidence/runs/tx4/sim_drna.err
+27f7f92631e6130e985e562a9ef119bec22ba6458f78a0fb3bfd15125c7a7bf4  evidence/runs/tx4/sim_drna.time
+ef45f763a905d70f277a281c987aa386f39d62cd121275390fcbda44ad0b339a  evidence/scripts/tx_bench.sh
+4feccc36aabe4eba92fd98829f9f3f85b48192f32d45bdb6992505fc19579bd1  evidence/scripts/tx_quant_compare.py
+1814d4364452dbecdeb61898946e7449b162df210a7e1fd8935378a29e9cffcc  evidence/scripts/tx_sim_truth.py
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/ledger.tsv b/docs/validation/2026-10-21-transcriptome/evidence/ledger.tsv
new file mode 100755
index 0000000..d0ce0c7
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/ledger.tsv
@@ -0,0 +1,5 @@
+mm2	cdna wall=184.67 cpu=2285.03 unmapped=1987	drna wall=105.69 cpu=1026.26 unmapped=37838	sim_cdna wall=47.19 cpu=441.83  mapped 99.89% primary on true transcript 93.73% on true gene 99.53% true transcript among alignments 99.89%	sim_drna wall=38.16 cpu=396.32  mapped 99.69% primary on true transcript 91.98% on true gene 99.33% true transcript among alignments 99.68%
+dna_N100	cdna wall=146.33 cpu=1535.12 unmapped=2493 transcripts: 21,271 with reads; reads 79,110 vs 78,331; Pearson 0.99893, log2 0.96622, Spearman 0.93590; reassigned 1,287 (1.63%) genes: 9,541 with reads; reads 79,110 vs 78,331; Pearson 0.99937, log2 0.99374, Spearman 0.99247; reassigned 515 (0.65%) 	drna wall=102.42 cpu=1032.07 unmapped=39115 transcripts: 27,353 with reads; reads 143,105 vs 141,931; Pearson 0.99900, log2 0.97835, Spearman 0.94488; reassigned 1,820 (1.27%) genes: 10,948 with reads; reads 143,105 vs 141,931; Pearson 0.99968, log2 0.99484, Spearman 0.99371; reassigned 792 (0.55%) 	sim_cdna wall=31.68 cpu=296.84  mapped 99.85% primary on true transcript 93.89% on true gene 99.48% true transcript among alignments 99.85%	sim_drna wall=31.99 cpu=293.60  mapped 98.82% primary on true transcript 91.33% on true gene 98.49% true transcript among alignments 98.80%
+tx1	cdna wall=183.68 cpu=2039.95 unmapped=1987 transcripts: 21,306 with reads; reads 79,110 vs 78,211; Pearson 0.99912, log2 0.96374, Spearman 0.92857; reassigned 1,380 (1.74%) genes: 9,532 with reads; reads 79,110 vs 78,211; Pearson 0.99950, log2 0.99472, Spearman 0.99366; reassigned 523 (0.66%) 	drna wall=101.63 cpu=1246.68 unmapped=37838 transcripts: 27,227 with reads; reads 143,105 vs 142,590; Pearson 0.99939, log2 0.98103, Spearman 0.95013; reassigned 1,334 (0.93%) genes: 10,925 with reads; reads 143,105 vs 142,590; Pearson 0.99997, log2 0.99755, Spearman 0.99693; reassigned 354 (0.25%) 	sim_cdna wall=45.58 cpu=418.40  mapped 99.89% primary on true transcript 93.88% on true gene 99.53% true transcript among alignments 99.89%	sim_drna wall=37.63 cpu=363.29  mapped 99.69% primary on true transcript 92.17% on true gene 99.34% true transcript among alignments 99.68%
+tx3	cdna wall=85.15 cpu=1193.59 unmapped=1987 transcripts: 21,306 with reads; reads 79,110 vs 78,211; Pearson 0.99912, log2 0.96374, Spearman 0.92856; reassigned 1,380 (1.74%) genes: 9,532 with reads; reads 79,110 vs 78,211; Pearson 0.99950, log2 0.99472, Spearman 0.99364; reassigned 523 (0.66%) 	drna wall=38.90 cpu=506.41 unmapped=37838 transcripts: 27,227 with reads; reads 143,105 vs 142,590; Pearson 0.99939, log2 0.98103, Spearman 0.95013; reassigned 1,334 (0.93%) genes: 10,925 with reads; reads 143,105 vs 142,590; Pearson 0.99997, log2 0.99755, Spearman 0.99693; reassigned 354 (0.25%) 	sim_cdna wall=20.41 cpu=227.59  mapped 99.89% primary on true transcript 93.88% on true gene 99.53% true transcript among alignments 99.89%	sim_drna wall=18.53 cpu=183.47  mapped 99.69% primary on true transcript 92.17% on true gene 99.34% true transcript among alignments 99.68%
+tx4	cdna wall=81.22 cpu=1148.77 unmapped=1987 transcripts: 21,306 with reads; reads 79,110 vs 78,211; Pearson 0.99912, log2 0.96374, Spearman 0.92856; reassigned 1,380 (1.74%) genes: 9,532 with reads; reads 79,110 vs 78,211; Pearson 0.99950, log2 0.99472, Spearman 0.99365; reassigned 523 (0.66%) 	drna wall=37.30 cpu=484.92 unmapped=37838 transcripts: 27,227 with reads; reads 143,105 vs 142,590; Pearson 0.99939, log2 0.98103, Spearman 0.95013; reassigned 1,334 (0.93%) genes: 10,925 with reads; reads 143,105 vs 142,590; Pearson 0.99997, log2 0.99755, Spearman 0.99693; reassigned 354 (0.25%) 	sim_cdna wall=19.80 cpu=219.74  mapped 99.89% primary on true transcript 93.88% on true gene 99.53% true transcript among alignments 99.89%	sim_drna wall=18.09 cpu=175.25  mapped 99.69% primary on true transcript 92.17% on true gene 99.34% true transcript among alignments 99.68%
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.err
new file mode 100755
index 0000000..56bfa3b
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.bonefish.raw...
+[*] Loaded part 1 in 0.058s — k: 19; w: 19; #seq: 533740; total len: 946309864
+[*] Mapped 200000 reads in 146.237s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.oarfish.log b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.oarfish.log
new file mode 100755
index 0000000..adbe82b
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.oarfish.log
@@ -0,0 +1,37 @@
+2026-10-21T22:19:01.762111Z  INFO oarfish: setting filters to nanocount defaults.
+2026-10-21T22:19:01.966191Z  INFO oarfish::alignment_parser: read header from BAM file cdna.q.bam, contains 533,740 reference sequences.
+2026-10-21T22:19:01.966394Z  INFO oarfish::alignment_parser: saw supported mapper rammap as a program in the header; proceeding.
+2026-10-21T22:19:01.966413Z  INFO oarfish::util::digest_utils: calculating seqcol digest
+2026-10-21T22:19:03.352014Z  INFO oarfish::util::digest_utils: done calculating seqcol digest
+2026-10-21T22:19:03.399509Z  INFO oarfish: parsed reference information for 533,740 transcripts.
+2026-10-21T22:19:05.936523Z  INFO oarfish::alignment_parser: the alignment file contained 2,493 unmapped read records.
+2026-10-21T22:19:05.937428Z  INFO oarfish::bulk: Parsing of alignments from input took: 2s 537ms 727us 759ns
+2026-10-21T22:19:05.937502Z  INFO oarfish::bulk: 
+discard_table: 
+╭─────────────────────────────────┬─────────╮
+│ reason                          │ count   │
+├─────────────────────────────────┼─────────┤
+│ too far from 5' end             │ 0       │
+│ too far from 3' end             │ 461285  │
+│ score too low                   │ 455915  │
+│ aligned fraction too low        │ 6057    │
+│ aligned length too short        │ 270     │
+│ inconsistent orientation        │ 1532440 │
+│ supplementary alignment         │ 12166   │
+│ read had no mapping             │ 0       │
+│ read had no valid alignment     │ 113119  │
+│ reads with valid best alignment │ 78331   │
+╰─────────────────────────────────┴─────────╯
+
+2026-10-21T22:19:05.937535Z  INFO oarfish::bulk: Total number of alignment records : 506,247
+2026-10-21T22:19:05.937556Z  INFO oarfish::bulk: number of aligned reads : 78,331
+2026-10-21T22:19:05.937575Z  INFO oarfish::bulk: number of unique alignments : 16,398
+2026-10-21T22:19:06.121495Z  INFO oarfish::em: iteration 100; rel diff 0.006687934315578949
+2026-10-21T22:19:06.309666Z  INFO oarfish::em: iteration 200; rel diff 0.0030421754005212145
+2026-10-21T22:19:06.500129Z  INFO oarfish::em: iteration 300; rel diff 0.0027460575988249723
+2026-10-21T22:19:06.683627Z  INFO oarfish::em: iteration 400; rel diff 0.0024077160823059766
+2026-10-21T22:19:06.865898Z  INFO oarfish::em: iteration 500; rel diff 0.0020442441605902054
+2026-10-21T22:19:07.052350Z  INFO oarfish::em: iteration 600; rel diff 0.0016790329612567613
+2026-10-21T22:19:07.234089Z  INFO oarfish::em: iteration 700; rel diff 0.0013360158155703073
+2026-10-21T22:19:07.411224Z  INFO oarfish::em: iteration 800; rel diff 0.0010336219741871734
+2026-10-21T22:19:07.778245Z  INFO oarfish: oarfish completed successfully.
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.oarfish.meta_info.json b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.oarfish.meta_info.json
new file mode 100755
index 0000000..cde72ca
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.oarfish.meta_info.json
@@ -0,0 +1,61 @@
+{
+  "prob_model": "no_coverage",
+  "alignment_source": "from_bam",
+  "alignment_time": {
+    "comment": "Time to parse (in alignment mode) or generate (in raw read mode) alignments, as well as apply filters, and compute conditional probabilities.",
+    "human_time": "2s 537ms 727us 759ns",
+    "seconds": 2.537727759
+  },
+  "bin_width": 100,
+  "filter_options": {
+    "five_prime_clip": 4294967295,
+    "three_prime_clip": 50,
+    "score_threshold": 0.949999988079071,
+    "min_aligned_fraction": 0.5,
+    "min_aligned_len": 50,
+    "which_strand": "Forward",
+    "model_coverage": false,
+    "logistic_growth_rate": 2.0,
+    "write_assignment_probs": false,
+    "write_assignment_probs_type": null,
+    "score_prob_denom": 5.0
+  },
+  "discard_table": {
+    "discard_5p": 0,
+    "discard_3p": 461285,
+    "discard_score": 455915,
+    "discard_aln_frac": 6057,
+    "discard_aln_len": 270,
+    "discard_ori": 1532440,
+    "discard_supp": 12166,
+    "no_mapping": 0,
+    "no_valid_aln": 113119,
+    "valid_best_aln": 78331
+  },
+  "alignments": "cdna.q.bam",
+  "output": "cdna.oarfish",
+  "verbose": false,
+  "single_cell": false,
+  "quiet": false,
+  "em_max_iter": 1000,
+  "em_convergence_thresh": 0.001,
+  "threads": 16,
+  "filter_group": "NanocountFilters",
+  "write_assignment_probs": null,
+  "short_quant": null,
+  "num_bootstraps": 0,
+  "digest": {
+    "bam_digest": {
+      "seqcol_digest": {
+        "level": 1,
+        "names": "JtpXbvlLRu6PIRtExJYCjpWt-HJCdlmY",
+        "lengths": "0af0dJPuoZAGSA1OxTC98WvOUDqyABTS",
+        "sorted_name_length_pairs": "obf7zAUChfwy1NNRVLcMGbXvxOeWlK7P"
+      },
+      "sha256_digests": {
+        "sha256_names": "a36bb3e27e5844f319bb15d352c86e85df88a5e8f6cc82781434eac34ce725b5",
+        "sha256_seqs": null
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.time
new file mode 100755
index 0000000..26296cb
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/cdna.time
@@ -0,0 +1 @@
+146.33 1521.47 13.65 4282160
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.err
new file mode 100755
index 0000000..14a47de
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.bonefish.raw...
+[*] Loaded part 1 in 0.057s — k: 19; w: 19; #seq: 533740; total len: 946309864
+[*] Mapped 200000 reads in 102.377s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.oarfish.log b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.oarfish.log
new file mode 100755
index 0000000..c099e08
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.oarfish.log
@@ -0,0 +1,37 @@
+2026-10-21T22:20:58.905339Z  INFO oarfish: setting filters to nanocount defaults.
+2026-10-21T22:20:59.455788Z  INFO oarfish::alignment_parser: read header from BAM file drna.q.bam, contains 533,740 reference sequences.
+2026-10-21T22:20:59.456015Z  INFO oarfish::alignment_parser: saw supported mapper rammap as a program in the header; proceeding.
+2026-10-21T22:20:59.456099Z  INFO oarfish::util::digest_utils: calculating seqcol digest
+2026-10-21T22:21:01.037731Z  INFO oarfish::util::digest_utils: done calculating seqcol digest
+2026-10-21T22:21:01.087342Z  INFO oarfish: parsed reference information for 533,740 transcripts.
+2026-10-21T22:21:02.783703Z  INFO oarfish::alignment_parser: the alignment file contained 39,115 unmapped read records.
+2026-10-21T22:21:02.784604Z  INFO oarfish::bulk: Parsing of alignments from input took: 1s 697ms 51us 619ns
+2026-10-21T22:21:02.784683Z  INFO oarfish::bulk: 
+discard_table: 
+╭─────────────────────────────────┬────────╮
+│ reason                          │ count  │
+├─────────────────────────────────┼────────┤
+│ too far from 5' end             │ 0      │
+│ too far from 3' end             │ 447021 │
+│ score too low                   │ 617833 │
+│ aligned fraction too low        │ 3667   │
+│ aligned length too short        │ 429    │
+│ inconsistent orientation        │ 19775  │
+│ supplementary alignment         │ 8963   │
+│ read had no mapping             │ 0      │
+│ read had no valid alignment     │ 15287  │
+│ reads with valid best alignment │ 141931 │
+╰─────────────────────────────────┴────────╯
+
+2026-10-21T22:21:02.784719Z  INFO oarfish::bulk: Total number of alignment records : 902,842
+2026-10-21T22:21:02.784743Z  INFO oarfish::bulk: number of aligned reads : 141,931
+2026-10-21T22:21:02.784764Z  INFO oarfish::bulk: number of unique alignments : 33,138
+2026-10-21T22:21:03.051876Z  INFO oarfish::em: iteration 100; rel diff 0.010536816603753867
+2026-10-21T22:21:03.319086Z  INFO oarfish::em: iteration 200; rel diff 0.004419448920463556
+2026-10-21T22:21:03.603201Z  INFO oarfish::em: iteration 300; rel diff 0.0031571401822824063
+2026-10-21T22:21:03.896206Z  INFO oarfish::em: iteration 400; rel diff 0.0021467043918845007
+2026-10-21T22:21:04.185293Z  INFO oarfish::em: iteration 500; rel diff 0.0017786512610291755
+2026-10-21T22:21:04.478971Z  INFO oarfish::em: iteration 600; rel diff 0.0015069623348835158
+2026-10-21T22:21:04.758486Z  INFO oarfish::em: iteration 700; rel diff 0.0012990544237337647
+2026-10-21T22:21:05.030935Z  INFO oarfish::em: iteration 800; rel diff 0.0011007552935052263
+2026-10-21T22:21:05.526318Z  INFO oarfish: oarfish completed successfully.
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.oarfish.meta_info.json b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.oarfish.meta_info.json
new file mode 100755
index 0000000..7216635
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.oarfish.meta_info.json
@@ -0,0 +1,61 @@
+{
+  "prob_model": "no_coverage",
+  "alignment_source": "from_bam",
+  "alignment_time": {
+    "comment": "Time to parse (in alignment mode) or generate (in raw read mode) alignments, as well as apply filters, and compute conditional probabilities.",
+    "human_time": "1s 697ms 51us 619ns",
+    "seconds": 1.697051619
+  },
+  "bin_width": 100,
+  "filter_options": {
+    "five_prime_clip": 4294967295,
+    "three_prime_clip": 50,
+    "score_threshold": 0.949999988079071,
+    "min_aligned_fraction": 0.5,
+    "min_aligned_len": 50,
+    "which_strand": "Forward",
+    "model_coverage": false,
+    "logistic_growth_rate": 2.0,
+    "write_assignment_probs": false,
+    "write_assignment_probs_type": null,
+    "score_prob_denom": 5.0
+  },
+  "discard_table": {
+    "discard_5p": 0,
+    "discard_3p": 447021,
+    "discard_score": 617833,
+    "discard_aln_frac": 3667,
+    "discard_aln_len": 429,
+    "discard_ori": 19775,
+    "discard_supp": 8963,
+    "no_mapping": 0,
+    "no_valid_aln": 15287,
+    "valid_best_aln": 141931
+  },
+  "alignments": "drna.q.bam",
+  "output": "drna.oarfish",
+  "verbose": false,
+  "single_cell": false,
+  "quiet": false,
+  "em_max_iter": 1000,
+  "em_convergence_thresh": 0.001,
+  "threads": 16,
+  "filter_group": "NanocountFilters",
+  "write_assignment_probs": null,
+  "short_quant": null,
+  "num_bootstraps": 0,
+  "digest": {
+    "bam_digest": {
+      "seqcol_digest": {
+        "level": 1,
+        "names": "JtpXbvlLRu6PIRtExJYCjpWt-HJCdlmY",
+        "lengths": "0af0dJPuoZAGSA1OxTC98WvOUDqyABTS",
+        "sorted_name_length_pairs": "obf7zAUChfwy1NNRVLcMGbXvxOeWlK7P"
+      },
+      "sha256_digests": {
+        "sha256_names": "a36bb3e27e5844f319bb15d352c86e85df88a5e8f6cc82781434eac34ce725b5",
+        "sha256_seqs": null
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.time
new file mode 100755
index 0000000..d428ad4
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/drna.time
@@ -0,0 +1 @@
+102.42 1022.63 9.44 3816724
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_cdna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_cdna.err
new file mode 100755
index 0000000..f98c3eb
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_cdna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.bonefish.raw...
+[*] Loaded part 1 in 0.072s — k: 19; w: 19; #seq: 533740; total len: 946309864
+[*] Mapped 44667 reads in 31.629s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_cdna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_cdna.time
new file mode 100755
index 0000000..0f132ad
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_cdna.time
@@ -0,0 +1 @@
+31.68 294.12 2.72 2966044
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_drna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_drna.err
new file mode 100755
index 0000000..6bb90bb
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_drna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.bonefish.raw...
+[*] Loaded part 1 in 0.056s — k: 19; w: 19; #seq: 533740; total len: 946309864
+[*] Mapped 44787 reads in 31.935s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_drna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_drna.time
new file mode 100755
index 0000000..462835b
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/dna_N100/sim_drna.time
@@ -0,0 +1 @@
+31.99 290.91 2.69 3017908
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.err
new file mode 100755
index 0000000..b6fcd49
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.err
@@ -0,0 +1,8 @@
+[M::main::1.479*0.93] loaded/built the index for 533740 target sequence(s)
+[M::mm_mapopt_update::1.769*0.94] mid_occ = 321
+[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 533740
+[M::mm_idx_stat::1.937*0.95] distinct minimizers: 24494645 (35.25% are singletons); average occurrences: 7.157; average spacing: 5.398; total length: 946309864
+[M::worker_pipeline::184.518*12.38] mapped 200000 sequences
+[M::main] Version: 2.31-r1302
+[M::main] CMD: minimap2 -ax map-ont -N 100 --eqx -t 16 ${DATA}/rna/tx/tx.mm2.mmi ${DATA}/rna/cdna_hg002_200k.fq.gz
+[M::main] Real time: 184.565 sec; CPU: 2284.936 sec; Peak RSS: 6.224 GB
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.oarfish.log b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.oarfish.log
new file mode 100755
index 0000000..c57d23d
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.oarfish.log
@@ -0,0 +1,39 @@
+2026-10-21T22:12:45.930338Z  INFO oarfish: setting filters to nanocount defaults.
+2026-10-21T22:12:47.255912Z  INFO oarfish::alignment_parser: read header from BAM file cdna.q.bam, contains 533,740 reference sequences.
+2026-10-21T22:12:47.256039Z  INFO oarfish::alignment_parser: saw supported mapper minimap2 as a program in the header; proceeding.
+2026-10-21T22:12:47.256069Z  INFO oarfish::util::digest_utils: calculating seqcol digest
+2026-10-21T22:12:48.723814Z  INFO oarfish::util::digest_utils: done calculating seqcol digest
+2026-10-21T22:12:48.778644Z  INFO oarfish: parsed reference information for 533,740 transcripts.
+2026-10-21T22:12:51.457417Z  INFO oarfish::alignment_parser: the alignment file contained 1,987 unmapped read records.
+2026-10-21T22:12:51.458428Z  INFO oarfish::bulk: Parsing of alignments from input took: 2s 679ms 677us 675ns
+2026-10-21T22:12:51.458491Z  INFO oarfish::bulk: 
+discard_table: 
+╭─────────────────────────────────┬─────────╮
+│ reason                          │ count   │
+├─────────────────────────────────┼─────────┤
+│ too far from 5' end             │ 0       │
+│ too far from 3' end             │ 462883  │
+│ score too low                   │ 490021  │
+│ aligned fraction too low        │ 6006    │
+│ aligned length too short        │ 512     │
+│ inconsistent orientation        │ 1577719 │
+│ supplementary alignment         │ 11758   │
+│ read had no mapping             │ 0       │
+│ read had no valid alignment     │ 112897  │
+│ reads with valid best alignment │ 79110   │
+╰─────────────────────────────────┴─────────╯
+
+2026-10-21T22:12:51.458521Z  INFO oarfish::bulk: Total number of alignment records : 514,935
+2026-10-21T22:12:51.458538Z  INFO oarfish::bulk: number of aligned reads : 79,110
+2026-10-21T22:12:51.458554Z  INFO oarfish::bulk: number of unique alignments : 16,364
+2026-10-21T22:12:51.728608Z  INFO oarfish::em: iteration 100; rel diff 0.007166221619798012
+2026-10-21T22:12:52.000959Z  INFO oarfish::em: iteration 200; rel diff 0.0035408263878241334
+2026-10-21T22:12:52.293597Z  INFO oarfish::em: iteration 300; rel diff 0.0031280216458239142
+2026-10-21T22:12:52.556885Z  INFO oarfish::em: iteration 400; rel diff 0.0029273414618858477
+2026-10-21T22:12:52.808543Z  INFO oarfish::em: iteration 500; rel diff 0.00267875229554468
+2026-10-21T22:12:53.062457Z  INFO oarfish::em: iteration 600; rel diff 0.0023856855923007725
+2026-10-21T22:12:53.326400Z  INFO oarfish::em: iteration 700; rel diff 0.0020596900205139055
+2026-10-21T22:12:53.576518Z  INFO oarfish::em: iteration 800; rel diff 0.0017197054445243875
+2026-10-21T22:12:53.861055Z  INFO oarfish::em: iteration 900; rel diff 0.0013881675124502997
+2026-10-21T22:12:54.117372Z  INFO oarfish::em: iteration 1,000; rel diff 0.0010853914191092447
+2026-10-21T22:12:54.620657Z  INFO oarfish: oarfish completed successfully.
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.oarfish.meta_info.json b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.oarfish.meta_info.json
new file mode 100755
index 0000000..fbb4d79
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.oarfish.meta_info.json
@@ -0,0 +1,61 @@
+{
+  "prob_model": "no_coverage",
+  "alignment_source": "from_bam",
+  "alignment_time": {
+    "comment": "Time to parse (in alignment mode) or generate (in raw read mode) alignments, as well as apply filters, and compute conditional probabilities.",
+    "human_time": "2s 679ms 677us 675ns",
+    "seconds": 2.6796776749999998
+  },
+  "bin_width": 100,
+  "filter_options": {
+    "five_prime_clip": 4294967295,
+    "three_prime_clip": 50,
+    "score_threshold": 0.949999988079071,
+    "min_aligned_fraction": 0.5,
+    "min_aligned_len": 50,
+    "which_strand": "Forward",
+    "model_coverage": false,
+    "logistic_growth_rate": 2.0,
+    "write_assignment_probs": false,
+    "write_assignment_probs_type": null,
+    "score_prob_denom": 5.0
+  },
+  "discard_table": {
+    "discard_5p": 0,
+    "discard_3p": 462883,
+    "discard_score": 490021,
+    "discard_aln_frac": 6006,
+    "discard_aln_len": 512,
+    "discard_ori": 1577719,
+    "discard_supp": 11758,
+    "no_mapping": 0,
+    "no_valid_aln": 112897,
+    "valid_best_aln": 79110
+  },
+  "alignments": "cdna.q.bam",
+  "output": "cdna.oarfish",
+  "verbose": false,
+  "single_cell": false,
+  "quiet": false,
+  "em_max_iter": 1000,
+  "em_convergence_thresh": 0.001,
+  "threads": 16,
+  "filter_group": "NanocountFilters",
+  "write_assignment_probs": null,
+  "short_quant": null,
+  "num_bootstraps": 0,
+  "digest": {
+    "bam_digest": {
+      "seqcol_digest": {
+        "level": 1,
+        "names": "JtpXbvlLRu6PIRtExJYCjpWt-HJCdlmY",
+        "lengths": "0af0dJPuoZAGSA1OxTC98WvOUDqyABTS",
+        "sorted_name_length_pairs": "obf7zAUChfwy1NNRVLcMGbXvxOeWlK7P"
+      },
+      "sha256_digests": {
+        "sha256_names": "a36bb3e27e5844f319bb15d352c86e85df88a5e8f6cc82781434eac34ce725b5",
+        "sha256_seqs": null
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.time
new file mode 100755
index 0000000..162df5f
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/cdna.time
@@ -0,0 +1 @@
+184.67 2274.58 10.45 6525996
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.err
new file mode 100755
index 0000000..3c83301
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.err
@@ -0,0 +1,8 @@
+[M::main::1.568*0.90] loaded/built the index for 533740 target sequence(s)
+[M::mm_mapopt_update::1.864*0.92] mid_occ = 321
+[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 533740
+[M::mm_idx_stat::2.033*0.92] distinct minimizers: 24494645 (35.25% are singletons); average occurrences: 7.157; average spacing: 5.398; total length: 946309864
+[M::worker_pipeline::105.558*9.72] mapped 200000 sequences
+[M::main] Version: 2.31-r1302
+[M::main] CMD: minimap2 -ax map-ont -N 100 --eqx -t 16 ${DATA}/rna/tx/tx.mm2.mmi ${DATA}/rna/drna_hg002_200k.fq.gz
+[M::main] Real time: 105.607 sec; CPU: 1026.178 sec; Peak RSS: 4.956 GB
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.oarfish.log b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.oarfish.log
new file mode 100755
index 0000000..b6ab93c
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.oarfish.log
@@ -0,0 +1,37 @@
+2026-10-21T22:14:47.836713Z  INFO oarfish: setting filters to nanocount defaults.
+2026-10-21T22:14:48.324842Z  INFO oarfish::alignment_parser: read header from BAM file drna.q.bam, contains 533,740 reference sequences.
+2026-10-21T22:14:48.324939Z  INFO oarfish::alignment_parser: saw supported mapper minimap2 as a program in the header; proceeding.
+2026-10-21T22:14:48.324964Z  INFO oarfish::util::digest_utils: calculating seqcol digest
+2026-10-21T22:14:49.624816Z  INFO oarfish::util::digest_utils: done calculating seqcol digest
+2026-10-21T22:14:49.679233Z  INFO oarfish: parsed reference information for 533,740 transcripts.
+2026-10-21T22:14:51.559986Z  INFO oarfish::alignment_parser: the alignment file contained 37,838 unmapped read records.
+2026-10-21T22:14:51.560861Z  INFO oarfish::bulk: Parsing of alignments from input took: 1s 881ms 500us 349ns
+2026-10-21T22:14:51.560943Z  INFO oarfish::bulk: 
+discard_table: 
+╭─────────────────────────────────┬────────╮
+│ reason                          │ count  │
+├─────────────────────────────────┼────────┤
+│ too far from 5' end             │ 0      │
+│ too far from 3' end             │ 448545 │
+│ score too low                   │ 685706 │
+│ aligned fraction too low        │ 3709   │
+│ aligned length too short        │ 1269   │
+│ inconsistent orientation        │ 26528  │
+│ supplementary alignment         │ 8810   │
+│ read had no mapping             │ 0      │
+│ read had no valid alignment     │ 15348  │
+│ reads with valid best alignment │ 143105 │
+╰─────────────────────────────────┴────────╯
+
+2026-10-21T22:14:51.560976Z  INFO oarfish::bulk: Total number of alignment records : 915,447
+2026-10-21T22:14:51.561000Z  INFO oarfish::bulk: number of aligned reads : 143,105
+2026-10-21T22:14:51.561022Z  INFO oarfish::bulk: number of unique alignments : 32,841
+2026-10-21T22:14:51.927465Z  INFO oarfish::em: iteration 100; rel diff 0.01053681660375387
+2026-10-21T22:14:52.304491Z  INFO oarfish::em: iteration 200; rel diff 0.004420918597068916
+2026-10-21T22:14:52.694024Z  INFO oarfish::em: iteration 300; rel diff 0.0031571401822710642
+2026-10-21T22:14:53.099404Z  INFO oarfish::em: iteration 400; rel diff 0.0021467043918847344
+2026-10-21T22:14:53.497974Z  INFO oarfish::em: iteration 500; rel diff 0.001778651261029389
+2026-10-21T22:14:53.903052Z  INFO oarfish::em: iteration 600; rel diff 0.0015069623348832968
+2026-10-21T22:14:54.277297Z  INFO oarfish::em: iteration 700; rel diff 0.001299054423733763
+2026-10-21T22:14:54.650960Z  INFO oarfish::em: iteration 800; rel diff 0.001100755293505225
+2026-10-21T22:14:55.302345Z  INFO oarfish: oarfish completed successfully.
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.oarfish.meta_info.json b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.oarfish.meta_info.json
new file mode 100755
index 0000000..db96e1b
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.oarfish.meta_info.json
@@ -0,0 +1,61 @@
+{
+  "prob_model": "no_coverage",
+  "alignment_source": "from_bam",
+  "alignment_time": {
+    "comment": "Time to parse (in alignment mode) or generate (in raw read mode) alignments, as well as apply filters, and compute conditional probabilities.",
+    "human_time": "1s 881ms 500us 349ns",
+    "seconds": 1.881500349
+  },
+  "bin_width": 100,
+  "filter_options": {
+    "five_prime_clip": 4294967295,
+    "three_prime_clip": 50,
+    "score_threshold": 0.949999988079071,
+    "min_aligned_fraction": 0.5,
+    "min_aligned_len": 50,
+    "which_strand": "Forward",
+    "model_coverage": false,
+    "logistic_growth_rate": 2.0,
+    "write_assignment_probs": false,
+    "write_assignment_probs_type": null,
+    "score_prob_denom": 5.0
+  },
+  "discard_table": {
+    "discard_5p": 0,
+    "discard_3p": 448545,
+    "discard_score": 685706,
+    "discard_aln_frac": 3709,
+    "discard_aln_len": 1269,
+    "discard_ori": 26528,
+    "discard_supp": 8810,
+    "no_mapping": 0,
+    "no_valid_aln": 15348,
+    "valid_best_aln": 143105
+  },
+  "alignments": "drna.q.bam",
+  "output": "drna.oarfish",
+  "verbose": false,
+  "single_cell": false,
+  "quiet": false,
+  "em_max_iter": 1000,
+  "em_convergence_thresh": 0.001,
+  "threads": 16,
+  "filter_group": "NanocountFilters",
+  "write_assignment_probs": null,
+  "short_quant": null,
+  "num_bootstraps": 0,
+  "digest": {
+    "bam_digest": {
+      "seqcol_digest": {
+        "level": 1,
+        "names": "JtpXbvlLRu6PIRtExJYCjpWt-HJCdlmY",
+        "lengths": "0af0dJPuoZAGSA1OxTC98WvOUDqyABTS",
+        "sorted_name_length_pairs": "obf7zAUChfwy1NNRVLcMGbXvxOeWlK7P"
+      },
+      "sha256_digests": {
+        "sha256_names": "a36bb3e27e5844f319bb15d352c86e85df88a5e8f6cc82781434eac34ce725b5",
+        "sha256_seqs": null
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.time
new file mode 100755
index 0000000..8a24812
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/drna.time
@@ -0,0 +1 @@
+105.69 1019.72 6.54 5197236
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_cdna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_cdna.err
new file mode 100755
index 0000000..bed9aa5
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_cdna.err
@@ -0,0 +1,8 @@
+[M::main::2.493*0.75] loaded/built the index for 533740 target sequence(s)
+[M::mm_mapopt_update::2.781*0.78] mid_occ = 321
+[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 533740
+[M::mm_idx_stat::2.950*0.79] distinct minimizers: 24494645 (35.25% are singletons); average occurrences: 7.157; average spacing: 5.398; total length: 946309864
+[M::worker_pipeline::47.065*9.39] mapped 44667 sequences
+[M::main] Version: 2.31-r1302
+[M::main] CMD: minimap2 -ax map-ont -N 100 --eqx -t 16 ${DATA}/rna/tx/tx.mm2.mmi ${DATA}/rna/sim/sim_cdna.fq.gz
+[M::main] Real time: 47.091 sec; CPU: 441.736 sec; Peak RSS: 4.010 GB
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_cdna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_cdna.time
new file mode 100755
index 0000000..b03c381
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_cdna.time
@@ -0,0 +1 @@
+47.19 437.68 4.15 4204928
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_drna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_drna.err
new file mode 100755
index 0000000..60b8c1e
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_drna.err
@@ -0,0 +1,8 @@
+[M::main::2.042*0.81] loaded/built the index for 533740 target sequence(s)
+[M::mm_mapopt_update::2.395*0.84] mid_occ = 321
+[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 533740
+[M::mm_idx_stat::2.584*0.85] distinct minimizers: 24494645 (35.25% are singletons); average occurrences: 7.157; average spacing: 5.398; total length: 946309864
+[M::worker_pipeline::38.039*10.42] mapped 44787 sequences
+[M::main] Version: 2.31-r1302
+[M::main] CMD: minimap2 -ax map-ont -N 100 --eqx -t 16 ${DATA}/rna/tx/tx.mm2.mmi ${DATA}/rna/sim/sim_drna.fq.gz
+[M::main] Real time: 38.073 sec; CPU: 396.242 sec; Peak RSS: 4.285 GB
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_drna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_drna.time
new file mode 100755
index 0000000..4ec34bb
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/mm2/sim_drna.time
@@ -0,0 +1 @@
+38.16 392.60 3.72 4492936
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.err
new file mode 100755
index 0000000..58780b0
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.082s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 200000 reads in 183.603s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.oarfish.log b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.oarfish.log
new file mode 100755
index 0000000..2b4fa35
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.oarfish.log
@@ -0,0 +1,37 @@
+2026-10-21T22:25:30.849141Z  INFO oarfish: setting filters to nanocount defaults.
+2026-10-21T22:25:31.487266Z  INFO oarfish::alignment_parser: read header from BAM file cdna.q.bam, contains 533,740 reference sequences.
+2026-10-21T22:25:31.487375Z  INFO oarfish::alignment_parser: saw supported mapper rammap as a program in the header; proceeding.
+2026-10-21T22:25:31.487397Z  INFO oarfish::util::digest_utils: calculating seqcol digest
+2026-10-21T22:25:33.278578Z  INFO oarfish::util::digest_utils: done calculating seqcol digest
+2026-10-21T22:25:33.331749Z  INFO oarfish: parsed reference information for 533,740 transcripts.
+2026-10-21T22:25:36.080207Z  INFO oarfish::alignment_parser: the alignment file contained 1,987 unmapped read records.
+2026-10-21T22:25:36.081394Z  INFO oarfish::bulk: Parsing of alignments from input took: 2s 749ms 534us 747ns
+2026-10-21T22:25:36.081512Z  INFO oarfish::bulk: 
+discard_table: 
+╭─────────────────────────────────┬─────────╮
+│ reason                          │ count   │
+├─────────────────────────────────┼─────────┤
+│ too far from 5' end             │ 0       │
+│ too far from 3' end             │ 484078  │
+│ score too low                   │ 470973  │
+│ aligned fraction too low        │ 6842    │
+│ aligned length too short        │ 597     │
+│ inconsistent orientation        │ 1583343 │
+│ supplementary alignment         │ 14706   │
+│ read had no mapping             │ 0       │
+│ read had no valid alignment     │ 112960  │
+│ reads with valid best alignment │ 78211   │
+╰─────────────────────────────────┴─────────╯
+
+2026-10-21T22:25:36.081585Z  INFO oarfish::bulk: Total number of alignment records : 506,048
+2026-10-21T22:25:36.081603Z  INFO oarfish::bulk: number of aligned reads : 78,211
+2026-10-21T22:25:36.081615Z  INFO oarfish::bulk: number of unique alignments : 16,404
+2026-10-21T22:25:36.341782Z  INFO oarfish::em: iteration 100; rel diff 0.006687934315578947
+2026-10-21T22:25:36.593405Z  INFO oarfish::em: iteration 200; rel diff 0.0030421754005210814
+2026-10-21T22:25:36.852677Z  INFO oarfish::em: iteration 300; rel diff 0.002746057598825169
+2026-10-21T22:25:37.102096Z  INFO oarfish::em: iteration 400; rel diff 0.002407716082306436
+2026-10-21T22:25:37.361187Z  INFO oarfish::em: iteration 500; rel diff 0.0020442441605902067
+2026-10-21T22:25:37.597038Z  INFO oarfish::em: iteration 600; rel diff 0.001679032961256966
+2026-10-21T22:25:37.858003Z  INFO oarfish::em: iteration 700; rel diff 0.0013360158155701328
+2026-10-21T22:25:38.110912Z  INFO oarfish::em: iteration 800; rel diff 0.0010336219741874848
+2026-10-21T22:25:38.581135Z  INFO oarfish: oarfish completed successfully.
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.oarfish.meta_info.json b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.oarfish.meta_info.json
new file mode 100755
index 0000000..94316b6
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.oarfish.meta_info.json
@@ -0,0 +1,61 @@
+{
+  "prob_model": "no_coverage",
+  "alignment_source": "from_bam",
+  "alignment_time": {
+    "comment": "Time to parse (in alignment mode) or generate (in raw read mode) alignments, as well as apply filters, and compute conditional probabilities.",
+    "human_time": "2s 749ms 534us 747ns",
+    "seconds": 2.7495347470000002
+  },
+  "bin_width": 100,
+  "filter_options": {
+    "five_prime_clip": 4294967295,
+    "three_prime_clip": 50,
+    "score_threshold": 0.949999988079071,
+    "min_aligned_fraction": 0.5,
+    "min_aligned_len": 50,
+    "which_strand": "Forward",
+    "model_coverage": false,
+    "logistic_growth_rate": 2.0,
+    "write_assignment_probs": false,
+    "write_assignment_probs_type": null,
+    "score_prob_denom": 5.0
+  },
+  "discard_table": {
+    "discard_5p": 0,
+    "discard_3p": 484078,
+    "discard_score": 470973,
+    "discard_aln_frac": 6842,
+    "discard_aln_len": 597,
+    "discard_ori": 1583343,
+    "discard_supp": 14706,
+    "no_mapping": 0,
+    "no_valid_aln": 112960,
+    "valid_best_aln": 78211
+  },
+  "alignments": "cdna.q.bam",
+  "output": "cdna.oarfish",
+  "verbose": false,
+  "single_cell": false,
+  "quiet": false,
+  "em_max_iter": 1000,
+  "em_convergence_thresh": 0.001,
+  "threads": 16,
+  "filter_group": "NanocountFilters",
+  "write_assignment_probs": null,
+  "short_quant": null,
+  "num_bootstraps": 0,
+  "digest": {
+    "bam_digest": {
+      "seqcol_digest": {
+        "level": 1,
+        "names": "JtpXbvlLRu6PIRtExJYCjpWt-HJCdlmY",
+        "lengths": "0af0dJPuoZAGSA1OxTC98WvOUDqyABTS",
+        "sorted_name_length_pairs": "obf7zAUChfwy1NNRVLcMGbXvxOeWlK7P"
+      },
+      "sha256_digests": {
+        "sha256_names": "a36bb3e27e5844f319bb15d352c86e85df88a5e8f6cc82781434eac34ce725b5",
+        "sha256_seqs": null
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.time
new file mode 100755
index 0000000..d30eff8
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/cdna.time
@@ -0,0 +1 @@
+183.68 2025.44 14.51 4993332
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.err
new file mode 100755
index 0000000..87f7ef3
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.071s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 200000 reads in 101.582s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.oarfish.log b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.oarfish.log
new file mode 100755
index 0000000..aa97e69
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.oarfish.log
@@ -0,0 +1,37 @@
+2026-10-21T22:27:28.953675Z  INFO oarfish: setting filters to nanocount defaults.
+2026-10-21T22:27:29.310599Z  INFO oarfish::alignment_parser: read header from BAM file drna.q.bam, contains 533,740 reference sequences.
+2026-10-21T22:27:29.310694Z  INFO oarfish::alignment_parser: saw supported mapper rammap as a program in the header; proceeding.
+2026-10-21T22:27:29.310714Z  INFO oarfish::util::digest_utils: calculating seqcol digest
+2026-10-21T22:27:30.416792Z  INFO oarfish::util::digest_utils: done calculating seqcol digest
+2026-10-21T22:27:30.463774Z  INFO oarfish: parsed reference information for 533,740 transcripts.
+2026-10-21T22:27:32.205461Z  INFO oarfish::alignment_parser: the alignment file contained 37,838 unmapped read records.
+2026-10-21T22:27:32.206340Z  INFO oarfish::bulk: Parsing of alignments from input took: 1s 742ms 477us 78ns
+2026-10-21T22:27:32.206392Z  INFO oarfish::bulk: 
+discard_table: 
+╭─────────────────────────────────┬────────╮
+│ reason                          │ count  │
+├─────────────────────────────────┼────────┤
+│ too far from 5' end             │ 0      │
+│ too far from 3' end             │ 472740 │
+│ score too low                   │ 654768 │
+│ aligned fraction too low        │ 4076   │
+│ aligned length too short        │ 1281   │
+│ inconsistent orientation        │ 27194  │
+│ supplementary alignment         │ 10887  │
+│ read had no mapping             │ 0      │
+│ read had no valid alignment     │ 15496  │
+│ reads with valid best alignment │ 142590 │
+╰─────────────────────────────────┴────────╯
+
+2026-10-21T22:27:32.206423Z  INFO oarfish::bulk: Total number of alignment records : 908,590
+2026-10-21T22:27:32.206483Z  INFO oarfish::bulk: number of aligned reads : 142,590
+2026-10-21T22:27:32.206524Z  INFO oarfish::bulk: number of unique alignments : 33,000
+2026-10-21T22:27:32.556398Z  INFO oarfish::em: iteration 100; rel diff 0.010536816603753878
+2026-10-21T22:27:32.915011Z  INFO oarfish::em: iteration 200; rel diff 0.004420907414445859
+2026-10-21T22:27:33.290282Z  INFO oarfish::em: iteration 300; rel diff 0.0031571401822706093
+2026-10-21T22:27:33.709809Z  INFO oarfish::em: iteration 400; rel diff 0.0023764816476970715
+2026-10-21T22:27:34.119640Z  INFO oarfish::em: iteration 500; rel diff 0.0018667627046812466
+2026-10-21T22:27:34.508064Z  INFO oarfish::em: iteration 600; rel diff 0.0015069623348837274
+2026-10-21T22:27:34.894701Z  INFO oarfish::em: iteration 700; rel diff 0.0012990544237337618
+2026-10-21T22:27:35.218413Z  INFO oarfish::em: iteration 800; rel diff 0.0011007552935052244
+2026-10-21T22:27:36.037127Z  INFO oarfish: oarfish completed successfully.
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.oarfish.meta_info.json b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.oarfish.meta_info.json
new file mode 100755
index 0000000..f1eb427
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.oarfish.meta_info.json
@@ -0,0 +1,61 @@
+{
+  "prob_model": "no_coverage",
+  "alignment_source": "from_bam",
+  "alignment_time": {
+    "comment": "Time to parse (in alignment mode) or generate (in raw read mode) alignments, as well as apply filters, and compute conditional probabilities.",
+    "human_time": "1s 742ms 477us 78ns",
+    "seconds": 1.7424770779999998
+  },
+  "bin_width": 100,
+  "filter_options": {
+    "five_prime_clip": 4294967295,
+    "three_prime_clip": 50,
+    "score_threshold": 0.949999988079071,
+    "min_aligned_fraction": 0.5,
+    "min_aligned_len": 50,
+    "which_strand": "Forward",
+    "model_coverage": false,
+    "logistic_growth_rate": 2.0,
+    "write_assignment_probs": false,
+    "write_assignment_probs_type": null,
+    "score_prob_denom": 5.0
+  },
+  "discard_table": {
+    "discard_5p": 0,
+    "discard_3p": 472740,
+    "discard_score": 654768,
+    "discard_aln_frac": 4076,
+    "discard_aln_len": 1281,
+    "discard_ori": 27194,
+    "discard_supp": 10887,
+    "no_mapping": 0,
+    "no_valid_aln": 15496,
+    "valid_best_aln": 142590
+  },
+  "alignments": "drna.q.bam",
+  "output": "drna.oarfish",
+  "verbose": false,
+  "single_cell": false,
+  "quiet": false,
+  "em_max_iter": 1000,
+  "em_convergence_thresh": 0.001,
+  "threads": 16,
+  "filter_group": "NanocountFilters",
+  "write_assignment_probs": null,
+  "short_quant": null,
+  "num_bootstraps": 0,
+  "digest": {
+    "bam_digest": {
+      "seqcol_digest": {
+        "level": 1,
+        "names": "JtpXbvlLRu6PIRtExJYCjpWt-HJCdlmY",
+        "lengths": "0af0dJPuoZAGSA1OxTC98WvOUDqyABTS",
+        "sorted_name_length_pairs": "obf7zAUChfwy1NNRVLcMGbXvxOeWlK7P"
+      },
+      "sha256_digests": {
+        "sha256_names": "a36bb3e27e5844f319bb15d352c86e85df88a5e8f6cc82781434eac34ce725b5",
+        "sha256_seqs": null
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.time
new file mode 100755
index 0000000..dbd421f
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/drna.time
@@ -0,0 +1 @@
+101.63 1237.44 9.24 4765836
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_cdna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_cdna.err
new file mode 100755
index 0000000..7c17635
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_cdna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.056s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 44667 reads in 45.543s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_cdna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_cdna.time
new file mode 100755
index 0000000..d1e5ba1
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_cdna.time
@@ -0,0 +1 @@
+45.58 414.99 3.41 4006160
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_drna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_drna.err
new file mode 100755
index 0000000..dd48a2d
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_drna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.073s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 44787 reads in 37.571s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_drna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_drna.time
new file mode 100755
index 0000000..d554531
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx1/sim_drna.time
@@ -0,0 +1 @@
+37.63 360.25 3.04 3998448
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.err
new file mode 100755
index 0000000..a8acaae
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.056s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 200000 reads in 85.094s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.oarfish.log b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.oarfish.log
new file mode 100755
index 0000000..0df72cb
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.oarfish.log
@@ -0,0 +1,37 @@
+2026-10-21T23:13:49.362976Z  INFO oarfish: setting filters to nanocount defaults.
+2026-10-21T23:13:49.971278Z  INFO oarfish::alignment_parser: read header from BAM file cdna.q.bam, contains 533,740 reference sequences.
+2026-10-21T23:13:49.971511Z  INFO oarfish::alignment_parser: saw supported mapper rammap as a program in the header; proceeding.
+2026-10-21T23:13:49.971540Z  INFO oarfish::util::digest_utils: calculating seqcol digest
+2026-10-21T23:13:51.020221Z  INFO oarfish::util::digest_utils: done calculating seqcol digest
+2026-10-21T23:13:51.070087Z  INFO oarfish: parsed reference information for 533,740 transcripts.
+2026-10-21T23:13:53.654433Z  INFO oarfish::alignment_parser: the alignment file contained 1,987 unmapped read records.
+2026-10-21T23:13:53.655444Z  INFO oarfish::bulk: Parsing of alignments from input took: 2s 585ms 262us 302ns
+2026-10-21T23:13:53.655491Z  INFO oarfish::bulk: 
+discard_table: 
+╭─────────────────────────────────┬─────────╮
+│ reason                          │ count   │
+├─────────────────────────────────┼─────────┤
+│ too far from 5' end             │ 0       │
+│ too far from 3' end             │ 484078  │
+│ score too low                   │ 470973  │
+│ aligned fraction too low        │ 6842    │
+│ aligned length too short        │ 597     │
+│ inconsistent orientation        │ 1583343 │
+│ supplementary alignment         │ 14706   │
+│ read had no mapping             │ 0       │
+│ read had no valid alignment     │ 112960  │
+│ reads with valid best alignment │ 78211   │
+╰─────────────────────────────────┴─────────╯
+
+2026-10-21T23:13:53.655515Z  INFO oarfish::bulk: Total number of alignment records : 506,048
+2026-10-21T23:13:53.655527Z  INFO oarfish::bulk: number of aligned reads : 78,211
+2026-10-21T23:13:53.655539Z  INFO oarfish::bulk: number of unique alignments : 16,404
+2026-10-21T23:13:53.829419Z  INFO oarfish::em: iteration 100; rel diff 0.006687934315578945
+2026-10-21T23:13:54.002748Z  INFO oarfish::em: iteration 200; rel diff 0.0030421754005210836
+2026-10-21T23:13:54.183596Z  INFO oarfish::em: iteration 300; rel diff 0.0027460575988249736
+2026-10-21T23:13:54.358663Z  INFO oarfish::em: iteration 400; rel diff 0.00240771608230613
+2026-10-21T23:13:54.528410Z  INFO oarfish::em: iteration 500; rel diff 0.002044244160590207
+2026-10-21T23:13:54.697876Z  INFO oarfish::em: iteration 600; rel diff 0.0016790329612569657
+2026-10-21T23:13:54.869368Z  INFO oarfish::em: iteration 700; rel diff 0.0013360158155701321
+2026-10-21T23:13:55.040537Z  INFO oarfish::em: iteration 800; rel diff 0.0010336219741874848
+2026-10-21T23:13:55.412833Z  INFO oarfish: oarfish completed successfully.
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.oarfish.meta_info.json b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.oarfish.meta_info.json
new file mode 100755
index 0000000..d1a3b6b
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.oarfish.meta_info.json
@@ -0,0 +1,61 @@
+{
+  "prob_model": "no_coverage",
+  "alignment_source": "from_bam",
+  "alignment_time": {
+    "comment": "Time to parse (in alignment mode) or generate (in raw read mode) alignments, as well as apply filters, and compute conditional probabilities.",
+    "human_time": "2s 585ms 262us 302ns",
+    "seconds": 2.585262302
+  },
+  "bin_width": 100,
+  "filter_options": {
+    "five_prime_clip": 4294967295,
+    "three_prime_clip": 50,
+    "score_threshold": 0.949999988079071,
+    "min_aligned_fraction": 0.5,
+    "min_aligned_len": 50,
+    "which_strand": "Forward",
+    "model_coverage": false,
+    "logistic_growth_rate": 2.0,
+    "write_assignment_probs": false,
+    "write_assignment_probs_type": null,
+    "score_prob_denom": 5.0
+  },
+  "discard_table": {
+    "discard_5p": 0,
+    "discard_3p": 484078,
+    "discard_score": 470973,
+    "discard_aln_frac": 6842,
+    "discard_aln_len": 597,
+    "discard_ori": 1583343,
+    "discard_supp": 14706,
+    "no_mapping": 0,
+    "no_valid_aln": 112960,
+    "valid_best_aln": 78211
+  },
+  "alignments": "cdna.q.bam",
+  "output": "cdna.oarfish",
+  "verbose": false,
+  "single_cell": false,
+  "quiet": false,
+  "em_max_iter": 1000,
+  "em_convergence_thresh": 0.001,
+  "threads": 16,
+  "filter_group": "NanocountFilters",
+  "write_assignment_probs": null,
+  "short_quant": null,
+  "num_bootstraps": 0,
+  "digest": {
+    "bam_digest": {
+      "seqcol_digest": {
+        "level": 1,
+        "names": "JtpXbvlLRu6PIRtExJYCjpWt-HJCdlmY",
+        "lengths": "0af0dJPuoZAGSA1OxTC98WvOUDqyABTS",
+        "sorted_name_length_pairs": "obf7zAUChfwy1NNRVLcMGbXvxOeWlK7P"
+      },
+      "sha256_digests": {
+        "sha256_names": "a36bb3e27e5844f319bb15d352c86e85df88a5e8f6cc82781434eac34ce725b5",
+        "sha256_seqs": null
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.time
new file mode 100755
index 0000000..c18ecd6
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/cdna.time
@@ -0,0 +1 @@
+85.15 1187.15 6.44 5136416
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.err
new file mode 100755
index 0000000..672c9f4
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.053s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 200000 reads in 38.848s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.oarfish.log b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.oarfish.log
new file mode 100755
index 0000000..6dfbf7a
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.oarfish.log
@@ -0,0 +1,37 @@
+2026-10-21T23:14:42.280491Z  INFO oarfish: setting filters to nanocount defaults.
+2026-10-21T23:14:42.711417Z  INFO oarfish::alignment_parser: read header from BAM file drna.q.bam, contains 533,740 reference sequences.
+2026-10-21T23:14:42.711486Z  INFO oarfish::alignment_parser: saw supported mapper rammap as a program in the header; proceeding.
+2026-10-21T23:14:42.711503Z  INFO oarfish::util::digest_utils: calculating seqcol digest
+2026-10-21T23:14:43.843214Z  INFO oarfish::util::digest_utils: done calculating seqcol digest
+2026-10-21T23:14:43.890772Z  INFO oarfish: parsed reference information for 533,740 transcripts.
+2026-10-21T23:14:45.643414Z  INFO oarfish::alignment_parser: the alignment file contained 37,838 unmapped read records.
+2026-10-21T23:14:45.644280Z  INFO oarfish::bulk: Parsing of alignments from input took: 1s 753ms 443us 140ns
+2026-10-21T23:14:45.644351Z  INFO oarfish::bulk: 
+discard_table: 
+╭─────────────────────────────────┬────────╮
+│ reason                          │ count  │
+├─────────────────────────────────┼────────┤
+│ too far from 5' end             │ 0      │
+│ too far from 3' end             │ 472740 │
+│ score too low                   │ 654768 │
+│ aligned fraction too low        │ 4076   │
+│ aligned length too short        │ 1281   │
+│ inconsistent orientation        │ 27194  │
+│ supplementary alignment         │ 10887  │
+│ read had no mapping             │ 0      │
+│ read had no valid alignment     │ 15496  │
+│ reads with valid best alignment │ 142590 │
+╰─────────────────────────────────┴────────╯
+
+2026-10-21T23:14:45.644374Z  INFO oarfish::bulk: Total number of alignment records : 908,590
+2026-10-21T23:14:45.644386Z  INFO oarfish::bulk: number of aligned reads : 142,590
+2026-10-21T23:14:45.644398Z  INFO oarfish::bulk: number of unique alignments : 33,000
+2026-10-21T23:14:45.923126Z  INFO oarfish::em: iteration 100; rel diff 0.010536816603753874
+2026-10-21T23:14:46.182611Z  INFO oarfish::em: iteration 200; rel diff 0.004420907414445867
+2026-10-21T23:14:46.448334Z  INFO oarfish::em: iteration 300; rel diff 0.0031571401822707594
+2026-10-21T23:14:46.726713Z  INFO oarfish::em: iteration 400; rel diff 0.0023764816476970715
+2026-10-21T23:14:47.004955Z  INFO oarfish::em: iteration 500; rel diff 0.0018667627046812466
+2026-10-21T23:14:47.277195Z  INFO oarfish::em: iteration 600; rel diff 0.0015069623348837296
+2026-10-21T23:14:47.536203Z  INFO oarfish::em: iteration 700; rel diff 0.001299054423733764
+2026-10-21T23:14:47.791529Z  INFO oarfish::em: iteration 800; rel diff 0.0011007552935052257
+2026-10-21T23:14:48.271820Z  INFO oarfish: oarfish completed successfully.
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.oarfish.meta_info.json b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.oarfish.meta_info.json
new file mode 100755
index 0000000..8ebc933
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.oarfish.meta_info.json
@@ -0,0 +1,61 @@
+{
+  "prob_model": "no_coverage",
+  "alignment_source": "from_bam",
+  "alignment_time": {
+    "comment": "Time to parse (in alignment mode) or generate (in raw read mode) alignments, as well as apply filters, and compute conditional probabilities.",
+    "human_time": "1s 753ms 443us 140ns",
+    "seconds": 1.75344314
+  },
+  "bin_width": 100,
+  "filter_options": {
+    "five_prime_clip": 4294967295,
+    "three_prime_clip": 50,
+    "score_threshold": 0.949999988079071,
+    "min_aligned_fraction": 0.5,
+    "min_aligned_len": 50,
+    "which_strand": "Forward",
+    "model_coverage": false,
+    "logistic_growth_rate": 2.0,
+    "write_assignment_probs": false,
+    "write_assignment_probs_type": null,
+    "score_prob_denom": 5.0
+  },
+  "discard_table": {
+    "discard_5p": 0,
+    "discard_3p": 472740,
+    "discard_score": 654768,
+    "discard_aln_frac": 4076,
+    "discard_aln_len": 1281,
+    "discard_ori": 27194,
+    "discard_supp": 10887,
+    "no_mapping": 0,
+    "no_valid_aln": 15496,
+    "valid_best_aln": 142590
+  },
+  "alignments": "drna.q.bam",
+  "output": "drna.oarfish",
+  "verbose": false,
+  "single_cell": false,
+  "quiet": false,
+  "em_max_iter": 1000,
+  "em_convergence_thresh": 0.001,
+  "threads": 16,
+  "filter_group": "NanocountFilters",
+  "write_assignment_probs": null,
+  "short_quant": null,
+  "num_bootstraps": 0,
+  "digest": {
+    "bam_digest": {
+      "seqcol_digest": {
+        "level": 1,
+        "names": "JtpXbvlLRu6PIRtExJYCjpWt-HJCdlmY",
+        "lengths": "0af0dJPuoZAGSA1OxTC98WvOUDqyABTS",
+        "sorted_name_length_pairs": "obf7zAUChfwy1NNRVLcMGbXvxOeWlK7P"
+      },
+      "sha256_digests": {
+        "sha256_names": "a36bb3e27e5844f319bb15d352c86e85df88a5e8f6cc82781434eac34ce725b5",
+        "sha256_seqs": null
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.time
new file mode 100755
index 0000000..ba98a20
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/drna.time
@@ -0,0 +1 @@
+38.90 502.89 3.52 4842932
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_cdna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_cdna.err
new file mode 100755
index 0000000..6d530ab
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_cdna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.058s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 44667 reads in 20.369s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_cdna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_cdna.time
new file mode 100755
index 0000000..ec47479
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_cdna.time
@@ -0,0 +1 @@
+20.41 226.04 1.55 4006892
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_drna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_drna.err
new file mode 100755
index 0000000..09481cc
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_drna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.056s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 44787 reads in 18.479s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_drna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_drna.time
new file mode 100755
index 0000000..00ade84
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx3/sim_drna.time
@@ -0,0 +1 @@
+18.53 181.98 1.49 3996852
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.err
new file mode 100755
index 0000000..ad2dcb6
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.054s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 200000 reads in 81.158s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.oarfish.log b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.oarfish.log
new file mode 100755
index 0000000..e9dbfa2
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.oarfish.log
@@ -0,0 +1,37 @@
+2026-10-21T23:22:29.578604Z  INFO oarfish: setting filters to nanocount defaults.
+2026-10-21T23:22:30.163537Z  INFO oarfish::alignment_parser: read header from BAM file cdna.q.bam, contains 533,740 reference sequences.
+2026-10-21T23:22:30.163693Z  INFO oarfish::alignment_parser: saw supported mapper rammap as a program in the header; proceeding.
+2026-10-21T23:22:30.163721Z  INFO oarfish::util::digest_utils: calculating seqcol digest
+2026-10-21T23:22:31.127306Z  INFO oarfish::util::digest_utils: done calculating seqcol digest
+2026-10-21T23:22:31.173077Z  INFO oarfish: parsed reference information for 533,740 transcripts.
+2026-10-21T23:22:33.749556Z  INFO oarfish::alignment_parser: the alignment file contained 1,987 unmapped read records.
+2026-10-21T23:22:33.750439Z  INFO oarfish::bulk: Parsing of alignments from input took: 2s 577ms 240us 24ns
+2026-10-21T23:22:33.750504Z  INFO oarfish::bulk: 
+discard_table: 
+╭─────────────────────────────────┬─────────╮
+│ reason                          │ count   │
+├─────────────────────────────────┼─────────┤
+│ too far from 5' end             │ 0       │
+│ too far from 3' end             │ 484078  │
+│ score too low                   │ 470973  │
+│ aligned fraction too low        │ 6842    │
+│ aligned length too short        │ 597     │
+│ inconsistent orientation        │ 1583343 │
+│ supplementary alignment         │ 14706   │
+│ read had no mapping             │ 0       │
+│ read had no valid alignment     │ 112960  │
+│ reads with valid best alignment │ 78211   │
+╰─────────────────────────────────┴─────────╯
+
+2026-10-21T23:22:33.750528Z  INFO oarfish::bulk: Total number of alignment records : 506,048
+2026-10-21T23:22:33.750540Z  INFO oarfish::bulk: number of aligned reads : 78,211
+2026-10-21T23:22:33.750551Z  INFO oarfish::bulk: number of unique alignments : 16,404
+2026-10-21T23:22:33.978237Z  INFO oarfish::em: iteration 100; rel diff 0.006687934315579084
+2026-10-21T23:22:34.151374Z  INFO oarfish::em: iteration 200; rel diff 0.0030421754005210853
+2026-10-21T23:22:34.329616Z  INFO oarfish::em: iteration 300; rel diff 0.002746057598824974
+2026-10-21T23:22:34.499030Z  INFO oarfish::em: iteration 400; rel diff 0.00240771608230613
+2026-10-21T23:22:34.669623Z  INFO oarfish::em: iteration 500; rel diff 0.0020442441605902062
+2026-10-21T23:22:34.843810Z  INFO oarfish::em: iteration 600; rel diff 0.0016790329612569657
+2026-10-21T23:22:35.017640Z  INFO oarfish::em: iteration 700; rel diff 0.001336015815570133
+2026-10-21T23:22:35.191173Z  INFO oarfish::em: iteration 800; rel diff 0.001033621974187174
+2026-10-21T23:22:35.548327Z  INFO oarfish: oarfish completed successfully.
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.oarfish.meta_info.json b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.oarfish.meta_info.json
new file mode 100755
index 0000000..4e886c7
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.oarfish.meta_info.json
@@ -0,0 +1,61 @@
+{
+  "prob_model": "no_coverage",
+  "alignment_source": "from_bam",
+  "alignment_time": {
+    "comment": "Time to parse (in alignment mode) or generate (in raw read mode) alignments, as well as apply filters, and compute conditional probabilities.",
+    "human_time": "2s 577ms 240us 24ns",
+    "seconds": 2.577240024
+  },
+  "bin_width": 100,
+  "filter_options": {
+    "five_prime_clip": 4294967295,
+    "three_prime_clip": 50,
+    "score_threshold": 0.949999988079071,
+    "min_aligned_fraction": 0.5,
+    "min_aligned_len": 50,
+    "which_strand": "Forward",
+    "model_coverage": false,
+    "logistic_growth_rate": 2.0,
+    "write_assignment_probs": false,
+    "write_assignment_probs_type": null,
+    "score_prob_denom": 5.0
+  },
+  "discard_table": {
+    "discard_5p": 0,
+    "discard_3p": 484078,
+    "discard_score": 470973,
+    "discard_aln_frac": 6842,
+    "discard_aln_len": 597,
+    "discard_ori": 1583343,
+    "discard_supp": 14706,
+    "no_mapping": 0,
+    "no_valid_aln": 112960,
+    "valid_best_aln": 78211
+  },
+  "alignments": "cdna.q.bam",
+  "output": "cdna.oarfish",
+  "verbose": false,
+  "single_cell": false,
+  "quiet": false,
+  "em_max_iter": 1000,
+  "em_convergence_thresh": 0.001,
+  "threads": 16,
+  "filter_group": "NanocountFilters",
+  "write_assignment_probs": null,
+  "short_quant": null,
+  "num_bootstraps": 0,
+  "digest": {
+    "bam_digest": {
+      "seqcol_digest": {
+        "level": 1,
+        "names": "JtpXbvlLRu6PIRtExJYCjpWt-HJCdlmY",
+        "lengths": "0af0dJPuoZAGSA1OxTC98WvOUDqyABTS",
+        "sorted_name_length_pairs": "obf7zAUChfwy1NNRVLcMGbXvxOeWlK7P"
+      },
+      "sha256_digests": {
+        "sha256_names": "a36bb3e27e5844f319bb15d352c86e85df88a5e8f6cc82781434eac34ce725b5",
+        "sha256_seqs": null
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.time
new file mode 100755
index 0000000..d199741
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/cdna.time
@@ -0,0 +1 @@
+81.22 1142.58 6.19 5041368
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.err
new file mode 100755
index 0000000..7c159e9
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.058s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 200000 reads in 37.238s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.oarfish.log b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.oarfish.log
new file mode 100755
index 0000000..e5483de
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.oarfish.log
@@ -0,0 +1,37 @@
+2026-10-21T23:23:20.855165Z  INFO oarfish: setting filters to nanocount defaults.
+2026-10-21T23:23:21.330634Z  INFO oarfish::alignment_parser: read header from BAM file drna.q.bam, contains 533,740 reference sequences.
+2026-10-21T23:23:21.330782Z  INFO oarfish::alignment_parser: saw supported mapper rammap as a program in the header; proceeding.
+2026-10-21T23:23:21.330799Z  INFO oarfish::util::digest_utils: calculating seqcol digest
+2026-10-21T23:23:22.417163Z  INFO oarfish::util::digest_utils: done calculating seqcol digest
+2026-10-21T23:23:22.465806Z  INFO oarfish: parsed reference information for 533,740 transcripts.
+2026-10-21T23:23:24.210729Z  INFO oarfish::alignment_parser: the alignment file contained 37,838 unmapped read records.
+2026-10-21T23:23:24.211650Z  INFO oarfish::bulk: Parsing of alignments from input took: 1s 745ms 639us 706ns
+2026-10-21T23:23:24.211720Z  INFO oarfish::bulk: 
+discard_table: 
+╭─────────────────────────────────┬────────╮
+│ reason                          │ count  │
+├─────────────────────────────────┼────────┤
+│ too far from 5' end             │ 0      │
+│ too far from 3' end             │ 472740 │
+│ score too low                   │ 654768 │
+│ aligned fraction too low        │ 4076   │
+│ aligned length too short        │ 1281   │
+│ inconsistent orientation        │ 27194  │
+│ supplementary alignment         │ 10887  │
+│ read had no mapping             │ 0      │
+│ read had no valid alignment     │ 15496  │
+│ reads with valid best alignment │ 142590 │
+╰─────────────────────────────────┴────────╯
+
+2026-10-21T23:23:24.211750Z  INFO oarfish::bulk: Total number of alignment records : 908,590
+2026-10-21T23:23:24.211771Z  INFO oarfish::bulk: number of aligned reads : 142,590
+2026-10-21T23:23:24.211791Z  INFO oarfish::bulk: number of unique alignments : 33,000
+2026-10-21T23:23:24.462524Z  INFO oarfish::em: iteration 100; rel diff 0.010536816603753874
+2026-10-21T23:23:24.704591Z  INFO oarfish::em: iteration 200; rel diff 0.004420907414445402
+2026-10-21T23:23:24.964908Z  INFO oarfish::em: iteration 300; rel diff 0.0031571401822707555
+2026-10-21T23:23:25.235827Z  INFO oarfish::em: iteration 400; rel diff 0.0023764816476970715
+2026-10-21T23:23:25.500139Z  INFO oarfish::em: iteration 500; rel diff 0.0018667627046812466
+2026-10-21T23:23:25.756858Z  INFO oarfish::em: iteration 600; rel diff 0.0015069623348835139
+2026-10-21T23:23:26.014970Z  INFO oarfish::em: iteration 700; rel diff 0.0012990544237337638
+2026-10-21T23:23:26.260414Z  INFO oarfish::em: iteration 800; rel diff 0.0011007552935052253
+2026-10-21T23:23:26.738503Z  INFO oarfish: oarfish completed successfully.
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.oarfish.meta_info.json b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.oarfish.meta_info.json
new file mode 100755
index 0000000..9caceba
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.oarfish.meta_info.json
@@ -0,0 +1,61 @@
+{
+  "prob_model": "no_coverage",
+  "alignment_source": "from_bam",
+  "alignment_time": {
+    "comment": "Time to parse (in alignment mode) or generate (in raw read mode) alignments, as well as apply filters, and compute conditional probabilities.",
+    "human_time": "1s 745ms 639us 706ns",
+    "seconds": 1.745639706
+  },
+  "bin_width": 100,
+  "filter_options": {
+    "five_prime_clip": 4294967295,
+    "three_prime_clip": 50,
+    "score_threshold": 0.949999988079071,
+    "min_aligned_fraction": 0.5,
+    "min_aligned_len": 50,
+    "which_strand": "Forward",
+    "model_coverage": false,
+    "logistic_growth_rate": 2.0,
+    "write_assignment_probs": false,
+    "write_assignment_probs_type": null,
+    "score_prob_denom": 5.0
+  },
+  "discard_table": {
+    "discard_5p": 0,
+    "discard_3p": 472740,
+    "discard_score": 654768,
+    "discard_aln_frac": 4076,
+    "discard_aln_len": 1281,
+    "discard_ori": 27194,
+    "discard_supp": 10887,
+    "no_mapping": 0,
+    "no_valid_aln": 15496,
+    "valid_best_aln": 142590
+  },
+  "alignments": "drna.q.bam",
+  "output": "drna.oarfish",
+  "verbose": false,
+  "single_cell": false,
+  "quiet": false,
+  "em_max_iter": 1000,
+  "em_convergence_thresh": 0.001,
+  "threads": 16,
+  "filter_group": "NanocountFilters",
+  "write_assignment_probs": null,
+  "short_quant": null,
+  "num_bootstraps": 0,
+  "digest": {
+    "bam_digest": {
+      "seqcol_digest": {
+        "level": 1,
+        "names": "JtpXbvlLRu6PIRtExJYCjpWt-HJCdlmY",
+        "lengths": "0af0dJPuoZAGSA1OxTC98WvOUDqyABTS",
+        "sorted_name_length_pairs": "obf7zAUChfwy1NNRVLcMGbXvxOeWlK7P"
+      },
+      "sha256_digests": {
+        "sha256_names": "a36bb3e27e5844f319bb15d352c86e85df88a5e8f6cc82781434eac34ce725b5",
+        "sha256_seqs": null
+      }
+    }
+  }
+}
\ No newline at end of file
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.time
new file mode 100755
index 0000000..afd1d40
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/drna.time
@@ -0,0 +1 @@
+37.30 481.26 3.66 4865160
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_cdna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_cdna.err
new file mode 100755
index 0000000..1b5e67f
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_cdna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.054s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 44667 reads in 19.763s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_cdna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_cdna.time
new file mode 100755
index 0000000..7551d96
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_cdna.time
@@ -0,0 +1 @@
+19.80 218.22 1.52 4003232
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_drna.err b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_drna.err
new file mode 100755
index 0000000..57d07d3
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_drna.err
@@ -0,0 +1,3 @@
+[*] Loading index from ${DATA}/rna/tx/tx.tx.raw...
+[*] Loaded part 1 in 0.053s — k: 15; w: 10; #seq: 533740; total len: 946309864
+[*] Mapped 44787 reads in 18.054s (1 index part)
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_drna.time b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_drna.time
new file mode 100755
index 0000000..f5a2fda
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/runs/tx4/sim_drna.time
@@ -0,0 +1 @@
+18.09 173.81 1.44 3999960
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/scripts/tx_bench.sh b/docs/validation/2026-10-21-transcriptome/evidence/scripts/tx_bench.sh
new file mode 100755
index 0000000..80f7782
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/scripts/tx_bench.sh
@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+# Transcriptome-mapping benchmark: one build (BIN=minimap2 for the -x map-ont -N 100 --eqx baseline)
+# on HG002 cDNA / direct RNA 200k (speed, oarfish counts vs minimap2's) and simulated reads (truth).
+# Usage: tx_bench.sh LABEL BIN [extra args]; results in results/tx_quant/runs/LABEL, line in ledger.tsv.
+set -uo pipefail
+L=$1; BIN=$2; shift 2; EXTRA="$*"
+R=${BENCH}; D=$R/data/rna; X=$D/tx; O=$R/results/tx_quant/runs/$L; B=$R/results/tx_quant/runs/mm2
+export PATH=$HOME/micromamba/envs/vareval/bin:$HOME/micromamba/envs/ontaln/bin:$HOME/micromamba/envs/quant/bin:$PATH
+T=16; mkdir -p $O; cd $O
+declare -A READS=([cdna]=$D/cdna_hg002_200k.fq.gz [drna]=$D/drna_hg002_200k.fq.gz [sim_cdna]=$D/sim/sim_cdna.fq.gz [sim_drna]=$D/sim/sim_drna.fq.gz)
+if [[ $BIN == minimap2 ]]; then IDX=$X/tx.mm2.mmi; else IDX=${IDX:-$X/tx.tx.raw}; fi
+cat $IDX > /dev/null
+line="$L"
+for s in cdna drna sim_cdna sim_drna; do
+  if [[ $BIN == minimap2 ]]; then
+    /usr/bin/time -f "%e %U %S %M" -o $s.time minimap2 -ax map-ont -N 100 --eqx -t $T $IDX ${READS[$s]} 2> $s.err | samtools view -b -o $s.bam -
+  else
+    /usr/bin/time -f "%e %U %S %M" -o $s.time $BIN -a --eqx -t $T $EXTRA $IDX ${READS[$s]} 2> $s.err | samtools view -b -o $s.bam -
+  fi
+  read -r w u sy m < $s.time
+  line+="\t$s wall=$w cpu=$(echo "$u + $sy" | bc)"
+  if [[ $s == sim_* ]]; then
+    line+=" $(python3 $R/bench/tx_sim_truth.py ${READS[$s]} $s.bam | cut -d: -f2- | sed 's/  */ /g')"
+  else
+    # oarfish accepts only BAMs whose @PG names a validated aligner; relabel bonefish as rammap (its upstream).
+    samtools view -H $s.bam | sed 's/^@PG\tID:bonefish\tPN:bonefish/@PG\tID:rammap\tPN:rammap/' > hdr.sam
+    samtools reheader hdr.sam $s.bam > $s.q.bam && rm hdr.sam
+    oarfish -j $T -a $s.q.bam -o $s.oarfish --filter-group nanocount-filters > $s.oarfish.log 2>&1; rm -f $s.q.bam
+    line+=" unmapped=$(samtools view -c -f 4 $s.bam)"
+    [[ -s $B/$s.oarfish.quant && $L != mm2 ]] && line+=" $(python3 $R/bench/tx_quant_compare.py $B/$s.oarfish.quant $s.oarfish.quant | tr '\n' ' ' | sed 's/  */ /g')"
+  fi
+done
+echo -e "$line" | tee -a $R/results/tx_quant/ledger.tsv
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/scripts/tx_quant_compare.py b/docs/validation/2026-10-21-transcriptome/evidence/scripts/tx_quant_compare.py
new file mode 100644
index 0000000..85c1d9a
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/scripts/tx_quant_compare.py
@@ -0,0 +1,78 @@
+#!/usr/bin/env python3
+"""Compare oarfish quantifications from two aligners' transcriptome BAMs.
+
+Reads `<prefix>.quant` (tname, len, num_reads) of each, and prints Pearson correlation of counts and
+of log2(count + 1), Spearman correlation, and the share of reads assigned differently (half the sum
+of absolute count differences / total), at transcript and gene level (gene = 2nd |-field of the
+GENCODE transcript name). Only transcripts with at least one read in either run are compared.
+
+Usage: tx_quant_compare.py A.quant B.quant
+"""
+import math
+import sys
+
+
+def load(path):
+    d = {}
+    with open(path) as f:
+        header = f.readline().rstrip("\n").split("\t")
+        ci = header.index("num_reads") if "num_reads" in header else 2
+        for line in f:
+            x = line.rstrip("\n").split("\t")
+            d[x[0]] = float(x[ci])
+    return d
+
+
+def pearson(x, y):
+    n = len(x)
+    mx, my = sum(x) / n, sum(y) / n
+    sxy = sum((a - mx) * (b - my) for a, b in zip(x, y))
+    sx = math.sqrt(sum((a - mx) ** 2 for a in x))
+    sy = math.sqrt(sum((b - my) ** 2 for b in y))
+    return sxy / (sx * sy) if sx and sy else float("nan")
+
+
+def ranks(v):
+    order = sorted(range(len(v)), key=lambda i: v[i])
+    r = [0.0] * len(v)
+    i = 0
+    while i < len(v):
+        j = i
+        while j + 1 < len(v) and v[order[j + 1]] == v[order[i]]:
+            j += 1
+        for k in range(i, j + 1):
+            r[order[k]] = (i + j) / 2 + 1
+        i = j + 1
+    return r
+
+
+def report(name, a, b):
+    keys = [k for k in set(a) | set(b) if a.get(k, 0) > 0 or b.get(k, 0) > 0]
+    x = [a.get(k, 0.0) for k in keys]
+    y = [b.get(k, 0.0) for k in keys]
+    tot = sum(x)
+    diff = sum(abs(p - q) for p, q in zip(x, y)) / 2
+    lx = [math.log2(v + 1) for v in x]
+    ly = [math.log2(v + 1) for v in y]
+    print(f"{name}: {len(keys):,} with reads; reads {tot:,.0f} vs {sum(y):,.0f}; Pearson {pearson(x, y):.5f}, "
+          f"log2 {pearson(lx, ly):.5f}, Spearman {pearson(ranks(x), ranks(y)):.5f}; "
+          f"reassigned {diff:,.0f} ({100 * diff / max(tot, 1):.2f}%)")
+
+
+def gene_level(d):
+    g = {}
+    for k, v in d.items():
+        f = k.split("|")
+        gid = f[1] if len(f) > 1 else k
+        g[gid] = g.get(gid, 0.0) + v
+    return g
+
+
+def main():
+    a, b = load(sys.argv[1]), load(sys.argv[2])
+    report("transcripts", a, b)
+    report("genes", gene_level(a), gene_level(b))
+
+
+if __name__ == "__main__":
+    main()
diff --git a/docs/validation/2026-10-21-transcriptome/evidence/scripts/tx_sim_truth.py b/docs/validation/2026-10-21-transcriptome/evidence/scripts/tx_sim_truth.py
new file mode 100644
index 0000000..46ed9aa
--- /dev/null
+++ b/docs/validation/2026-10-21-transcriptome/evidence/scripts/tx_sim_truth.py
@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+"""Score transcriptome alignments of Badread reads simulated from GENCODE transcripts.
+
+Read names carry the source transcript (`ENST...|type|GENE,+strand,a-b`); reference names are
+GENCODE transcriptome headers (`ENST...|ENSG...|...|...|tx_name|GENE|len|type|`). Per BAM: reads
+mapped, primary on the true transcript, primary on a transcript of the true gene, and the true
+transcript among any of the read's alignments (what EM quantifiers use).
+
+Usage: tx_sim_truth.py READS.fq.gz A.bam [B.bam ...]
+"""
+import gzip
+import subprocess
+import sys
+
+
+def main():
+    truth = {}
+    with gzip.open(sys.argv[1], "rt") as fq:
+        for i, line in enumerate(fq):
+            if i % 4 == 0:
+                rid, _, desc = line[1:].rstrip("\n").partition(" ")
+                src = desc.split(",")[0].split("|")
+                truth[rid] = (src[0], src[2] if len(src) > 2 else "")
+    n = len(truth)
+    for bam in sys.argv[2:]:
+        prim = {}
+        anyhit = set()
+        p = subprocess.Popen(["samtools", "view", bam], stdout=subprocess.PIPE, text=True)
+        for line in p.stdout:
+            f = line.split("\t", 4)
+            flag = int(f[1])
+            if flag & 4 or f[0] not in truth:
+                continue
+            ref = f[2].split("|")
+            tx, gene = ref[0], ref[5] if len(ref) > 5 else ""
+            if tx == truth[f[0]][0]:
+                anyhit.add(f[0])
+            if not flag & 0x900:
+                prim[f[0]] = (tx, gene)
+        p.wait()
+        mapped = len(prim)
+        tx_ok = sum(prim[r][0] == truth[r][0] for r in prim)
+        gene_ok = sum(prim[r][1] == truth[r][1] for r in prim)
+        print(f"{bam}: mapped {100 * mapped / n:.2f}%  primary on true transcript {100 * tx_ok / n:.2f}%  "
+              f"on true gene {100 * gene_ok / n:.2f}%  true transcript among alignments {100 * len(anyhit) / n:.2f}%")
+
+
+if __name__ == "__main__":
+    main()
diff --git a/docs/validation/README.md b/docs/validation/README.md
index 20bcdfa..4356476 100644
--- a/docs/validation/README.md
+++ b/docs/validation/README.md
@@ -23,6 +23,7 @@ Each folder holds the README for one validation round, its evidence (logs, table
 | report | what |
 |---|---|
 | [2026-10-21-rna-cdna](2026-10-21-rna-cdna/README.md) | Direct RNA and cDNA (spliced presets) against minimap2, GENCODE and simulated reads |
+| [2026-10-21-transcriptome](2026-10-21-transcriptome/README.md) | Transcriptome mapping for quantification (`-x tx`, oarfish) |
 | [2026-10-20-metagenomics-duplex-rdna](2026-10-20-metagenomics-duplex-rdna/README.md) | Metagenome (Zymo fecal), HG002 duplex reads, rDNA |
 
 ## Speed, platforms and output