Issues

• Question: Correct orientation for 5p data

  COMBINE-lab/simpleaf#203 · Filter by author wmacnair opened on Jun 26, 2026
  1

• min-reads seems to have no effect in some cases

  COMBINE-lab/simpleaf#197 · Filter by author LinearParadox opened on May 20, 2026
  3

• Incorrect output with simpleaf flex-quant --chemistry 10x-flexv2-gex-3p

  COMBINE-lab/simpleaf#192 · Filter by author retogerber opened on Mar 20, 2026
  9

• Assigning similar genes where in multiplexed sample??? /10X 3-OCM with 2 species in one lane

  COMBINE-lab/simpleaf#184 · Filter by author polychronist opened on Oct 9, 2025

• Is VDJ analysis possible w/ simpleaf?

  COMBINE-lab/simpleaf#182 · Filter by author DrSunsation opened on Jul 3, 2025

• Further info on simpleaf index on HPCs

  COMBINE-lab/simpleaf#181 · Filter by author wmacnair opened on Mar 20, 2025
  2

• how to do with complex barcodes or multi linked barcode

  COMBINE-lab/simpleaf#176 · Filter by author d-jch opened on Jan 10, 2025
  1

• simpleaf index: runtime expectations

  COMBINE-lab/simpleaf#166 · Filter by author kevinrue opened on Nov 19, 2024
  6

• run simpleaf with a different umi length (here 9) | add-chemistry successfully

  COMBINE-lab/simpleaf#164 · Filter by author robertzeibich opened on Nov 11, 2024

• simpleaf index error piscem index failed to build succesfully ExitStatus(unix_wait_status(6))

  COMBINE-lab/simpleaf#163 · Filter by author lichtobergo opened on Nov 4, 2024

• [feature request] umi-edit-dist parameter

  COMBINE-lab/simpleaf#160 · Filter by author TavorB opened on Oct 17, 2024

• [feature request] 10x chemistry autodetection

  enhancementfeature
  COMBINE-lab/simpleaf#158 · Filter by author rob-p opened on Aug 8, 2024
  3

• Error: invalid base: 0067

  COMBINE-lab/simpleaf#137 · Filter by author holmrenser opened on Jun 4, 2024
  6

• [question]: maximum available parallelism and number of threads

  COMBINE-lab/simpleaf#135 · Filter by author tamuanand opened on Apr 1, 2024
  1

• 10x genomics FFPE chemistry

  COMBINE-lab/simpleaf#131 · Filter by author wangjiawen2013 opened on Feb 2, 2024

• Cell-by-isoform matrix

  COMBINE-lab/simpleaf#115 · Filter by author sameer-aryal opened on Oct 25, 2023
  2

• BD data

  COMBINE-lab/simpleaf#105 · Filter by author cathalgking opened on Sep 22, 2023
  4

• Processing SplitSeq / ParseBio data with simpleaf

  COMBINE-lab/simpleaf#104 · Filter by author wmacnair opened on Sep 18, 2023
  3

• CHM13 Index

  COMBINE-lab/simpleaf#100 · Filter by author AndrewSkelton opened on Aug 1, 2023