Issues

• Isoform proportions (gene avgTxLength) poorly reproducible between technical replicate libraries with 2x51/2x59 bp reads

  COMBINE-lab/salmon#1229 · Filter by author BenjaminDEMAILLE opened on Sep 29, 2026

• 2.6.0 audit remainder: the 3 unresolved #1140 items

  COMBINE-lab/salmon#1179 · Filter by author rob-p opened on Aug 24, 2026
  1

• In-memory RAD store for --radScratchDir (post-2.6.0): motivated by macOS and containers, not by speed

  COMBINE-lab/salmon#1168 · Filter by author rob-p opened on Aug 23, 2026

• Do the seed/chain anchor pathologies reach the scores quantification uses? (measurement: no, but right-orphan records report AS:i:0)

  COMBINE-lab/salmon#1152 · Filter by author BenjaminDEMAILLE opened on Aug 22, 2026

• Differences between softclip and softclipOverhangs

  COMBINE-lab/salmon#998 · Filter by author MarcelloMalpighi opened on Jan 23, 2026

• Can --keepDuplicates be enabled by default?

  COMBINE-lab/salmon#995 · Filter by author zhangwenda0518 opened on Nov 27, 2025

• Understanding large discrepancies between salmon counts and inferential replicate medians

  COMBINE-lab/salmon#994 · Filter by author JBrownBiostat opened on Nov 7, 2025

• CPU usage higher that rquested by --threads

  COMBINE-lab/salmon#993 · Filter by author bernt-matthias opened on Oct 29, 2025
  2

• alevin: missing quants.mat.gz or core dump

  COMBINE-lab/salmon#992 · Filter by author bernt-matthias opened on Oct 28, 2025
  2

• Latest releases missing

  COMBINE-lab/salmon#990 · Filter by author Stikus opened on Sep 16, 2025
  2

• Transcript quantification in salmon by merging de novo transcripts from IsoSeq SQANTI3 with known transcripts from Gencode

  COMBINE-lab/salmon#989 · Filter by author Motoufiq opened on Aug 11, 2025

• Compilation fails with clang19

  COMBINE-lab/salmon#988 · Filter by author outpaddling opened on Jul 26, 2025
  2

• How to understand --meta parameters

  COMBINE-lab/salmon#986 · Filter by author wfgui opened on Jul 8, 2025

• Salmon used in metagenomes

  COMBINE-lab/salmon#985 · Filter by author micro-hg-cpg opened on Jun 30, 2025

• Compiling problem

  COMBINE-lab/salmon#984 · Filter by author BioDNA-Research opened on Apr 16, 2025
  3

• Why does the Numreads have decimals?

  COMBINE-lab/salmon#983 · Filter by author powerfulDie opened on Apr 1, 2025
  1

• Missing (440) genes in Salmon output compared to GTF file

  COMBINE-lab/salmon#982 · Filter by author freekvh opened on Feb 26, 2025
  3

• --numRequiredObs Exception

  COMBINE-lab/salmon#981 · Filter by author aminor23 opened on Feb 17, 2025
  1

• Incorrect permissions on annotation GTF file cause segfault

  COMBINE-lab/salmon#980 · Filter by author alanhoyle opened on Feb 17, 2025
  1

• Latest release

  COMBINE-lab/salmon#979 · Filter by author Stikus opened on Feb 12, 2025
  1

• Doubts about using salmon quantitative results for unsupervised clustering.

  COMBINE-lab/salmon#978 · Filter by author xiaoguang-sjtu opened on Feb 12, 2025

• Salmon Discarding A Read in Pair

  COMBINE-lab/salmon#977 · Filter by author ericbretz opened on Jan 18, 2025

• Does lack of antisense lncRNAs in the reference affect quantification?

  COMBINE-lab/salmon#976 · Filter by author pasviber opened on Dec 18, 2024

• Error with salmon quant when filtering alignments by MAPQ

  COMBINE-lab/salmon#975 · Filter by author Taylorain opened on Dec 15, 2024

• best practices documentation on the ONT long reads

  COMBINE-lab/salmon#974 · Filter by author yinshiyi opened on Dec 9, 2024