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agat_sp_extract_sequences.pl different gffread

Status: Open.

#566 In NBISweden/AGAT;

· WWz33 opened on Oct 26, 2025

longest exon per gene above a threshold length

Status: Open.

#565 In NBISweden/AGAT;

· bioinfowheat opened on Oct 20, 2025

200k UTR created- is gff annotation or Agat correct?

Status: Open.

#563 In NBISweden/AGAT;

· desmodus1984 opened on Oct 8, 2025

introns are lost in GFF3 to GTF2.2 conversion

Status: Open.

#562 In NBISweden/AGAT;

· mrbertp opened on Oct 6, 2025

[BUG] GTF 'description' is not preserved during conversion.

Status: Open.

#561 In NBISweden/AGAT;

· marcguery opened on Sep 18, 2025

Feature request: Slight update to GTF 2.5 (GENCODE) format

Status: Open.

#560 In NBISweden/AGAT;

· mrendleman opened on Sep 17, 2025

empty attributes are appended to feature ID

Status: Open.

#556 In NBISweden/AGAT;

· Rik-149 opened on Aug 21, 2025

Make the scripts pipe-friendly (print messages to stderr if --output stdout)

Status: Open.

#553 In NBISweden/AGAT;

· kim-fehl opened on Jul 30, 2025

GFF to GTF modifies transcript_id

Status: Open.

#552 In NBISweden/AGAT;

· sivasubramanics opened on Jul 28, 2025

Is it possible to paralelize some scripts by running on subsets of GTF annotations?

Status: Open.

#545 In NBISweden/AGAT;

· dgruano opened on Jun 20, 2025

agat_convert_mfannot2gff.pl does not include LAGLIDADG, GIY and orfs in the gff file

Status: Open.

#533 In NBISweden/AGAT;

· GabrieleRigano99 opened on Apr 2, 2025

Add support for [X] cigar string on agat_convert_minimap2_bam2gff.pl

Status: Open.

#520 In NBISweden/AGAT;

· eggrandio opened on Jan 24, 2025