agat_sq_mask.pl

DESCRIPTION

The script masks (hard or soft) GFF-denoted segments out of a FASTA format file. It needs 3 input parameters: a gff3 file, a fasta file, and a Mask method. The result is written to the specified output file, or to STDOUT.

SYNOPSIS

agat_sq_mask.pl -g infile.gff -f infile.fasta  (-hm or -sm) [ -o outfile ]
agat_sq_mask.pl --help

OPTIONS

  • -g, --gff or -ref

    Input GTF/GFF file.

  • -f or --fasta

    Input fasta file that will be masked

  • -sm

    SoftMask option =>Sequences masked will be in lowercase

  • -hm

    HardMask option => Sequences masked will be replaced by a character. By default the character used is 'n'. But you are allowed to speceify any character of your choice. To use 'z' instead of 'n' type: -hm z

  • -o or --output

    Output GFF file. If no output file is specified, the output will be written to STDOUT.

  • -h or --help

    Display this helpful text.