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

Status: Open.

#496 In gpertea/stringtie;

· TingQi2020 opened on Nov 21, 2025

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

Status: Open.

#488 In gpertea/stringtie;

· Maria-Eduarda2024 opened on Sep 23, 2025

Stringite merge completely removing some tissue-specific gene models

Status: Open.

#487 In gpertea/stringtie;

· DustinSokolowski opened on Sep 17, 2025

Issues parsing GFF strand "?"

Status: Open.

#486 In gpertea/stringtie;

· Rik-149 opened on Sep 17, 2025

chechsum changed for stringtie v3.0.1

Status: Open.

#485 In gpertea/stringtie;

· daeho-ro opened on Sep 15, 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.

Status: Open.

#484 In gpertea/stringtie;

· YingLiPUMC opened on Sep 4, 2025

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

Status: Open.

#483 In gpertea/stringtie;

· RobAlbn opened on Sep 2, 2025

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

Status: Open.

#481 In gpertea/stringtie;

· yinshiyi opened on Aug 8, 2025

Stringtie3 exon number of negative strand is in wrong order

Status: Open.

#479 In gpertea/stringtie;

· SophieEhres opened on Jul 30, 2025

Stringtie take a very long time to compute and never end

Status: Open.

#477 In gpertea/stringtie;

· wdesaintjean opened on Jul 25, 2025

FPKM computed on gene effective length or annotation length?

Status: Open.

#474 In gpertea/stringtie;

· bhdobrin opened on Jul 3, 2025

error parsing -s (mono-exonic coverage)

Status: Open.

#473 In gpertea/stringtie;

· noncodo opened on Jun 27, 2025