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.

• -h or --help

  Display this helpful text.