agat_sq_mask.pl¶
DESCRIPTION¶
The script masks GFF-denoted segments out of a FASTA format file. This script masks (hard or soft) repeats among sequences. 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.