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Add better labeled intermediate file output from transcriptome and flair fusion

Status: Open.

#665 In BrooksLabUCSC/flair;

· cafelton opened on Jul 16, 2026

Isoform content differs when aligning to transcriptome reference compared to when aligning to genome (and post-processing with FLAIR)

Status: Open.

#661 In BrooksLabUCSC/flair;

· lgraciamaz opened on Jun 16, 2026

Test FLAIR fusion on non-human data

Status: Open.

#658 In BrooksLabUCSC/flair;

· cafelton opened on May 21, 2026

Add transcriptome tests with non-gencode annotations

Status: Open.

#657 In BrooksLabUCSC/flair;

· cafelton opened on May 21, 2026

diffsplice_fishers_exact error: cannot import name 'main' from 'flair.diffsplice_fishers_exact'

Status: Open.

#652 In BrooksLabUCSC/flair;

· ZDD116 opened on May 8, 2026

FLAIR diffexp crashes when samples are not in continuous ordered groups

Status: Open.

#646 In BrooksLabUCSC/flair;

· cafelton opened on Apr 3, 2026

default to discarding mono-exon transcripts that are not in annotation

Status: Open.

#642 In BrooksLabUCSC/flair;

· diekhans opened on Mar 24, 2026

flair_transcriptome thread usage exceeds expected allocation on HPC systems

Status: Open.

#640 In BrooksLabUCSC/flair;

· maxgmarin opened on Mar 19, 2026

issues with FLAIR align using splice junctions

Status: Open.

#633 In BrooksLabUCSC/flair;

· diekhans opened on Feb 27, 2026

FLAIR franscriptome should clearly document either a GTF or junctions file must be provide

Status: Open.

#632 In BrooksLabUCSC/flair;

· diekhans opened on Feb 18, 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