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simpleaf atac process fails at generate-permit-list with missing ref_lengths tag (ArrayU64)

Status: Open.

#204 In COMBINE-lab/simpleaf;

· caitlinottaway opened on Jul 7, 2026

Question: Correct orientation for 5p data

Status: Open.

#203 In COMBINE-lab/simpleaf;

· wmacnair opened on Jun 26, 2026

Add chemistry preset for GEM-X Flex v2 Configuration B (R1=28 / R2=90)

Status: Open.

#198 In COMBINE-lab/simpleaf;

· an-altosian opened on May 20, 2026

min-reads seems to have no effect in some cases

Status: Open.

#197 In COMBINE-lab/simpleaf;

· LinearParadox opened on May 20, 2026

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

Status: Open.

#192 In COMBINE-lab/simpleaf;

· retogerber opened on Mar 20, 2026

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

Status: Open.

#184 In COMBINE-lab/simpleaf;

· polychronist opened on Oct 9, 2025

Is VDJ analysis possible w/ simpleaf?

Status: Open.

#182 In COMBINE-lab/simpleaf;

· DrSunsation opened on Jul 3, 2025

Further info on simpleaf index on HPCs

Status: Open.

#181 In COMBINE-lab/simpleaf;

· wmacnair opened on Mar 20, 2025

how to do with complex barcodes or multi linked barcode

Status: Open.

#176 In COMBINE-lab/simpleaf;

· d-jch opened on Jan 10, 2025

simpleaf index: runtime expectations

Status: Open.

#166 In COMBINE-lab/simpleaf;

· kevinrue opened on Nov 19, 2024

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

Status: Open.

#164 In COMBINE-lab/simpleaf;

· robertzeibich opened on Nov 11, 2024

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

Status: Open.

#163 In COMBINE-lab/simpleaf;

· lichtobergo opened on Nov 4, 2024