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agat_sp_keep_longest_isoform.pl#

DESCRIPTION#

The script aims to filter isoforms when present. For a locus: - when all isoforms have CDS we keep the one with the longest CDS. - when some isoforms have CDS some others not, we keep the one with the longest CDS. - when none of the isoforms have CDS, we keep the one with the longest concatenated exons.

SYNOPSIS#

agat_sp_keep_longest_isoform.pl -gff file.gff  [ -o outfile ]
agat_sp_keep_longest_isoform.pl --help

OPTIONS#

  • --gff or -f

    GTF/GFF file.

  • --output or -o

    File where will be written the result. If no output file is specified, the output will be written to STDOUT.

  • -c or --config

    String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

  • -h or --help

    Display this helpful text.