Issues

• Long reads: strand from polyA tail, unstranded junction counts

  gpertea/stringtie#515 · Filter by author gpertea opened on Nov 13, 2026

• Long reads: deletions next to introns (follow-up to #513)

  gpertea/stringtie#514 · Filter by author gpertea opened on Nov 13, 2026
  1

• Implementation details of --merge mode in StringTie

  gpertea/stringtie#497 · Filter by author Bathroomboss opened on Jan 12, 2026

• Question Regarding Batch Effect Consideration in StringTie's Hybrid Assembly Mode

  gpertea/stringtie#496 · Filter by author TingQi2020 opened on Nov 21, 2025

• Some StringTie transcripts have no strand, causing SQANTI3 to discard them

  gpertea/stringtie#488 · Filter by author Maria-Eduarda2024 opened on Sep 23, 2025

• Stringite merge completely removing some tissue-specific gene models

  gpertea/stringtie#487 · Filter by author DustinSokolowski opened on Sep 17, 2025

• Issues parsing GFF strand "?"

  gpertea/stringtie#486 · Filter by author Rik-149 opened on Sep 17, 2025

• StringTie3 GTF file contains some genes and transcripts with biotype "artifact"

  gpertea/stringtie#483 · Filter by author RobAlbn opened on Sep 2, 2025

• -s (singlethr) is 4.75 or 1.5 when using -L ?

  gpertea/stringtie#481 · Filter by author yinshiyi opened on Aug 8, 2025
  1

• Stringtie3 exon number of negative strand is in wrong order

  gpertea/stringtie#479 · Filter by author SophieEhres opened on Jul 30, 2025

• Stringtie take a very long time to compute and never end

  gpertea/stringtie#477 · Filter by author wdesaintjean opened on Jul 25, 2025
  2

• FPKM computed on gene effective length or annotation length?

  gpertea/stringtie#474 · Filter by author bhdobrin opened on Jul 3, 2025

• error parsing -s (mono-exonic coverage)

  gpertea/stringtie#473 · Filter by author noncodo opened on Jun 27, 2025

• Intron length specification

  gpertea/stringtie#471 · Filter by author sanyalab opened on May 14, 2025

• Stringtie generates only single exon transcripts

  gpertea/stringtie#469 · Filter by author suz11001 opened on Apr 25, 2025
  3

• stringtie --merge joins overlapping transcripts even when they are on different strands

  bug
  gpertea/stringtie#468 · Filter by author m-jahn opened on Apr 22, 2025
  9

  

• Point features seem not to be used when predicting transcripts with option --ptf

  gpertea/stringtie#466 · Filter by author m-jahn opened on Apr 9, 2025
  2

• Segmentation fault with --mix option

  gpertea/stringtie#465 · Filter by author isabela42 opened on Apr 3, 2025
  14

• Key error when using prepDE.py

  gpertea/stringtie#463 · Filter by author melian98 opened on Feb 11, 2025
  3

• Issue with Zero Coverage for Some Exons/Transcripts in StringTie Despite Aligned Reads (Short Reads RNA-seq Analysis)

  gpertea/stringtie#462 · Filter by author fafaris39 opened on Jan 31, 2025
  1

• Use string merge to merge full-length transcript GTF file

  gpertea/stringtie#461 · Filter by author Tang-pro opened on Jan 19, 2025
  4

• Got 0 counts for all of the original genes from the reference gtf after 2nd round stringtie aligning to the merged gtf file?

  gpertea/stringtie#460 · Filter by author mt4614 opened on Jan 15, 2025

• Transcript ends are supported by low coverage

  gpertea/stringtie#459 · Filter by author MirkoBr opened on Jan 15, 2025
  11

• Use --mix with or without --rf ...?

  gpertea/stringtie#458 · Filter by author JohnUrban opened on Jan 10, 2025
  5

• Completion of error handling

  gpertea/stringtie#457 · Filter by author elfring opened on Jan 4, 2025