agat_sp_add_start_and_stop.pl.pl

DESCRIPTION

The script adds start and stop codons when a CDS feature exists. The script looks at the nucleotide sequence and checks the presence of start and stop codons. The script works even if the start or stop codon are split over several CDS features.

SYNOPSIS

agat_sp_add_start_and_stop.pl.pl --gff infile.gff --fasta genome.fa --out outfile.gff
agat_sp_add_start_and_stop.pl.pl --help

OPTIONS

  • --gff, -i or -g

    Input GTF/GFF file.

  • --fasta, --fa or -f

    Input fasta file. Needed to check that CDS sequences start by start codon and stop by stop codon.

  • --ct, --codon or --table

    Codon table to use. [default 1]

  • --out, --output or -o

    Output gff file updated

  • -v

    Verbose for debugging purpose.

  • --help or -h

    Display this helpful text.