agat_sp_add_intergenic_regions.pl

DESCRIPTION

The script aims to add intergenic features (intergenic_region) to gtf/gff file. The intergenic regions are deduced from gene features (feature type gene from the 3rd column).

SYNOPSIS

agat_sp_add_intergenic_regions.pl --gff infile --out outFile
agat_sp_add_intergenic_regions.pl --help

OPTIONS

• --gff, -f or --ref

  Input GTF/GFF file.

• --out, --output or -o

  Output file (default GFF3 - see config to modify output format).

• -c or --config

  String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently).

• -v or --verbose

  Add verbosity

• -h or --help

  Display this helpful text.