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stuck on salmon quant step

questionFurther information is requestedFurther information is requested

Status: Open.

#33 In plasslab/SCALPEL;

· nvivanco opened on Mar 4, 2026

Format of --clusters file

questionFurther information is requestedFurther information is requested

Status: Open.

#32 In plasslab/SCALPEL;

· guptas2005 opened on Feb 15, 2026

adding new samples

enhancementNew feature or requestNew feature or request

needs triage

Status: Open.

#31 In plasslab/SCALPEL;

· I-am-Shir opened on Feb 11, 2026

Issue Reading 10X GEX+ATAC Multiome Data

documentationImprovements or additions to documentationImprovements or additions to documentation

enhancementNew feature or requestNew feature or request

Status: Open.

#30 In plasslab/SCALPEL;

· guptas2005 opened on Feb 4, 2026

Unclear how to specify BAM files in sample sheet

questionFurther information is requestedFurther information is requested

Status: Open.

#29 In plasslab/SCALPEL;

· mschilli87 opened on Feb 2, 2026

The step for DGE and differential isoform usage is interrupted.

bugSomething isn't workingSomething isn't working

Status: Open.

#28 In plasslab/SCALPEL;

· Choeun-fran opened on Jan 26, 2026

Execution stops after skipping key processing steps

Status: Open.

#26 In plasslab/SCALPEL;

· Mangosteen24 opened on Dec 22, 2025

Better document that <code>*_ipriming_sites.bed.tar.gz</code> contains the same data as <code>*.polyA.track</code>

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#25 In plasslab/SCALPEL;

· mapostolides opened on Dec 12, 2025

Solution for the problem of the10x Chromium 3' scRNA-seq data stuck in the "salmon_bulk_quantification" step

questionFurther information is requestedFurther information is requested

staleThis is waiting for a response for a long time and it is not clear if it even is still relevant.This is waiting for a response for a long time and it is not clear if it even is still relevant.

Status: Open.

#23 In plasslab/SCALPEL;

· jinjinzh1190-cyber opened on Oct 16, 2025

Using STARsolo Output

enhancementNew feature or requestNew feature or request

Status: Open.

#22 In plasslab/SCALPEL;

· I-am-Shir opened on Oct 5, 2025