Issues

• [BUG] parse_counts() silently truncates fractional FL counts, zeroing low-expression transcripts

  triage
  ConesaLab/SQANTI3#624 · Filter by author DonGazpachoWR opened on Sep 14, 2026

• [BUG]

  triage
  ConesaLab/SQANTI3#622 · Filter by author as2110 opened on Aug 11, 2026
  2

• Question about SQANTI3 filtering false positive rate on RefSeq reference transcripts

  triage
  ConesaLab/SQANTI3#617 · Filter by author Xiaoguang-Shi opened on Jul 24, 2026

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

  triage
  ConesaLab/SQANTI3#614 · Filter by author developer-wellfishtech opened on Jun 26, 2026
  1

• [BUG] FL counts with incomplete transcript set

  triage
  ConesaLab/SQANTI3#613 · Filter by author ChrissiKalk97 opened on Jun 23, 2026

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

  triage
  ConesaLab/SQANTI3#611 · Filter by author tshori opened on Jun 18, 2026
  1

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

  triage
  ConesaLab/SQANTI3#585 · Filter by author GLagunas-Robles opened on Feb 25, 2026
  2

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

  triage
  ConesaLab/SQANTI3#575 · Filter by author leewqa opened on Feb 2, 2026
  3

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

  triage
  ConesaLab/SQANTI3#509 · Filter by author joelnitta opened on Aug 2, 2025
  3

• [BUG] Macaca fascicularis sqanti_qc.py error

  triage
  ConesaLab/SQANTI3#501 · Filter by author sfodel opened on Jul 23, 2025
  1

• [BUG] IsoAnnotLite assigns transcript ID as protein ID

  triage
  ConesaLab/SQANTI3#500 · Filter by author FabianJetzinger opened on Jul 15, 2025

• [BUG] Error using IsoAnnotLite with gencode gff3

  triage
  ConesaLab/SQANTI3#461 · Filter by author VandaLovejoy opened on May 9, 2025
  3

  

• [BUG] RTS Switching false negative

  triage
  ConesaLab/SQANTI3#441 · Filter by author Youpu-Chen opened on Apr 7, 2025
  1

  

• Option to write TSV for each report table

  enhancement
  ConesaLab/SQANTI3#218 · Filter by author diekhans opened on Aug 24, 2023
  3

• understanding the dup isoforms in the classification file

  QCquestion
  ConesaLab/SQANTI3#216 · Filter by author alexyfyf opened on Aug 23, 2023
  2