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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

agat_sp_flag_premature_stop_codons.pl mostly flags genes without premature stop codons

Status: Open.

#504 In NBISweden/AGAT;

· JWDebler opened on Oct 17, 2024

agat_convert_minimap2_bam2gff.pl handle Insertion and deletion

Status: Open.

#503 In NBISweden/AGAT;

· tjwu opened on Oct 8, 2024

Some transcripts are missing agat_convert_sp_gxf2gxf.pl

Status: Open.

#478 In NBISweden/AGAT;

· IrinaVKuznetsova opened on Aug 22, 2024

How to merge two genes with overlapping positions but no overlapping CDS?

Status: Open.

#468 In NBISweden/AGAT;

· BinZheng1998 opened on Jun 20, 2024

<code>agat_sp_extract_sequences.pl</code>: support for multicistronic transcripts.

Status: Open.

#451 In NBISweden/AGAT;

· jdcla opened on Apr 8, 2024

agat_sp_extract_sequences.pl does not incorporate CDS feature ID in headers

enhancementNew feature or requestNew feature or request

Status: Open.

#450 In NBISweden/AGAT;

· jdcla opened on Apr 8, 2024

Parsing of the X CIGAR code in bam files

Status: Open.

#422 In NBISweden/AGAT;

· sanyalab opened on Feb 7, 2024