All issues

Question about SQANTI3 filtering false positive rate on RefSeq reference transcripts

#617

· Xiaoguang-Shi opened

on Jul 24, 2026

[BUG] ORF prediction silently skipped despite no --skipORF flag — confusing interaction with --include_ORF

#614

· developer-wellfishtech opened

on Jun 26, 2026

[BUG] FL counts with incomplete transcript set

#613

· ChrissiKalk97 opened

on Jun 23, 2026

[BUG] Logger fails on docket due to a permission error

#611

· tshori opened

on Jun 18, 2026

[BUG] Sqanti3 Filter fails with an error when run with bioconda package (v6.0.1)

#609

· khersameesh24 opened

on Jun 1, 2026

[BUG] TD2.LongOrfs: not found when running SQANTI3 v6.0.1 from singularity (docker) container

#602

· skudashev opened

on Apr 27, 2026

[BUG] sqanti3_qc.py does not run with --genename enabled, but runs with the same gtf provided in --refGTF

#585

· GLagunas-Robles opened

on Feb 25, 2026

[BUG] IsoAnnotLite shows no transcripts were annotated despite running on provided ref gff3

#575

· leewqa opened

on Feb 2, 2026

[BUG] Error 'The 'gene_name' tag was not found in the input GTF file.' even though gene_name is in GTF file

#509

· joelnitta opened

on Aug 2, 2025

[BUG] Macaca fascicularis sqanti_qc.py error

#501

· sfodel opened

on Jul 23, 2025

[BUG] IsoAnnotLite assigns transcript ID as protein ID

#500

· FabianJetzinger opened

on Jul 15, 2025

[BUG] Error using IsoAnnotLite with gencode gff3

#461

· VandaLovejoy opened

on May 9, 2025