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Quantification instability after upgrading from v1.10.3 to v1.11.4

Status: Open.

#1011 In COMBINE-lab/salmon;

· Alexandra2022kzn opened on May 26, 2026

Differences between softclip and softclipOverhangs

Status: Open.

#998 In COMBINE-lab/salmon;

· MarcelloMalpighi opened on Jan 23, 2026

Can --keepDuplicates be enabled by default?

Status: Open.

#995 In COMBINE-lab/salmon;

· zhangwenda0518 opened on Nov 27, 2025

Understanding large discrepancies between salmon counts and inferential replicate medians

Status: Open.

#994 In COMBINE-lab/salmon;

· JBrownBiostat opened on Nov 7, 2025

CPU usage higher that rquested by --threads

Status: Open.

#993 In COMBINE-lab/salmon;

· bernt-matthias opened on Oct 29, 2025

alevin: missing quants.mat.gz or core dump

Status: Open.

#992 In COMBINE-lab/salmon;

· bernt-matthias opened on Oct 28, 2025

Latest releases missing

Status: Open.

#990 In COMBINE-lab/salmon;

· Stikus opened on Sep 16, 2025

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

Status: Open.

#989 In COMBINE-lab/salmon;

· Motoufiq opened on Aug 11, 2025

Compilation fails with clang19

Status: Open.

#988 In COMBINE-lab/salmon;

· outpaddling opened on Jul 26, 2025

How to understand --meta parameters

Status: Open.

#986 In COMBINE-lab/salmon;

· wfgui opened on Jul 8, 2025

Salmon used in metagenomes

Status: Open.

#985 In COMBINE-lab/salmon;

· micro-hg-cpg opened on Jun 30, 2025

Compiling problem

Status: Open.

#984 In COMBINE-lab/salmon;

· BioDNA-Research opened on Apr 16, 2025