Issues

• using stringtie -L on a bam with tag XS

  gpertea/stringtie#508 · Filter by author mhoang22 opened on Aug 20, 2026

• 2 rows for 1 gene ID in gene.abundance.txt

  gpertea/stringtie#506 · Filter by author mtochilkina opened on Jun 30, 2026
  1

• getting error of Illegal instruction (core dumped)

  gpertea/stringtie#504 · Filter by author trumanLuan opened on Apr 16, 2026

• Is stringtie able to distinguish endogenous from exogenous transcript?

  gpertea/stringtie#501 · Filter by author marionamujal opened on Feb 17, 2026

• -M parameter has to be set to 1.12 to predict transcript?

  gpertea/stringtie#500 · Filter by author JanaSperschneider opened on Feb 16, 2026

• Compatibility issues

  gpertea/stringtie#499 · Filter by author Jiashaoc opened on Jan 29, 2026

• Unstranded STAR Alignment with XS tags - reverse stranded assignment

  gpertea/stringtie#498 · Filter by author Riley-Grindle opened on Jan 27, 2026

• 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

• The key error and gene loss error in prepDE.py may be caused by the inconsistent number of transcripts in the gtf file output by stringtie -e.

  gpertea/stringtie#484 · Filter by author YingLiPUMC opened on Sep 4, 2025
  2

• 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