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<code>--remove_internal_priming</code> causes KeyError during firstpass transcriptomic alignment (FLAIR collapse v3.0.0b1)

Status: Open.

#629 In BrooksLabUCSC/flair;

· jibeomko opened on Feb 3, 2026

How to run diff_iso_usage with multiple samples per condition?

Status: Open.

#626 In BrooksLabUCSC/flair;

· evans-ZH opened on Jan 13, 2026

flair transcriptome: crashing with just one (of 20) alignments

Status: Open.

#623 In BrooksLabUCSC/flair;

· sklages opened on Dec 31, 2025

Flair combine exiting without any error, status says completed but no output files generated

mod; combine

Status: Open.

#622 In BrooksLabUCSC/flair;

· avani-binf opened on Dec 31, 2025

Flair correct crashing on one specific read conversion on hsa chr7; v3.0.0.b1

Status: Open.

#620 In BrooksLabUCSC/flair;

· semmrich opened on Dec 16, 2025

DiffSplice

Status: Open.

#615 In BrooksLabUCSC/flair;

· Juliaycliu opened on Nov 25, 2025

add option to create PDFs or SVGs to plot_isoform_usage

Status: Open.

#609 In BrooksLabUCSC/flair;

· diekhans opened on Nov 8, 2025

flair quantify

Status: Open.

#608 In BrooksLabUCSC/flair;

· ucsfpan opened on Nov 3, 2025

FLAIR stranding can be improved

Status: Open.

#600 In BrooksLabUCSC/flair;

· cafelton opened on Oct 21, 2025

diffexp and diffsplice errors

Status: Open.

#599 In BrooksLabUCSC/flair;

· olneykimberly opened on Oct 15, 2025

Why does flair quantify give results inconsistent with IGV?

Status: Open.

#597 In BrooksLabUCSC/flair;

· evans-ZH opened on Oct 14, 2025

ss1 &lt; ss2

Status: Open.

#596 In BrooksLabUCSC/flair;

· Geil625 opened on Oct 11, 2025