agat_sp_filter_by_mrnaBlastValue.pl

DESCRIPTION

The script aims to remove from a gff file all the sequence that have a similarity over THRESHOLD with another sequence (will keep only one). This is typically useful when creating a list of mRNA to use to train abinitio gene finder. A reciprocal blast of the sequences need to have been performed prior to the use of this script in order to get the blastp input file.

SYNOPSIS

agat_sp_filter_by_mrnaBlastValue.pl --gff infile.gff --blast blastfile --outfile outFile
agat_sp_filter_by_mrnaBlastValue.pl --help

OPTIONS

• --gff

  Input GTF/GFF file.

• --blast

  The list of the all-vs-all blast file (outfmt 6, blastp)

• --outfile

  The name of the output file. By default the output is the standard output.

• --help or -h

  Display this helpful text.