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Quantification with a --keepDuplicates index does not consistently distribute TPM/reads between duplicates

Status: Open.

#1008 In COMBINE-lab/salmon;

· vzhurov opened on May 13, 2026

Salmon Index Error: [locale::facet::_S_create_c_locale name not valid] despite setting LC_ALL

Status: Open.

#1006 In COMBINE-lab/salmon;

· hgod2356 opened on Apr 24, 2026

Option -d not recognized in salmon index 1.11.4

Status: Open.

#1005 In COMBINE-lab/salmon;

· nponts opened on Mar 17, 2026

Differences between softclip and softclipOverhangs

Status: Open.

#998 In COMBINE-lab/salmon;

· MarcelloMalpighi opened on Jan 23, 2026

std::bad_alloc on RHEL9

Status: Open.

#997 In COMBINE-lab/salmon;

· phupe opened on Jan 14, 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