agat_sp_flag_premature_stop_codons.pl

DESCRIPTION

The script flags the mRNAs containing premature stop codons. It will add the attribute "pseudo" and the value will be the positions of all premature stop codons. Gene are flagged as pseudogene only if all the isoforms are pseudogenes. The attribute will also be "pseudo" but will not contains any location.

SYNOPSIS

agat_sp_flag_premature_stop_codons.pl --gff infile.gff --fasta infile.fa --out outfile
agat_sp_flag_premature_stop_codons.pl --help

OPTIONS

• --gff, --ref or -reffile

  Input GTF/GFF file.

• -f, --fa or --fasta

  Imput fasta file.

• --ct, --codon or --table

  Codon table to use. [default 1]

• --out, --output or -o

  Output gff3 file where the result will be printed.

• --help or -h

  Display this helpful text.