agat_sp_separate_by_record_type.pl

DESCRIPTION

The script will separate the features from the gff input file into different files according to the record type. A record represent all features linked collectively by Parent/ID relationships. (e.g gene + mrna + exon + cds + utr of a locus).

a) When the record contains Level2 feature, the record type is the Level2 feature type (e.g tRNA,mRNA,ncRNA etc...) b) Some features do not have children (top and standalone level1 features) e.g. location,region,chromosome. In such case the record type is the level1 feature type.

SYNOPSIS

agat_sp_separate_by_record_type.pl -g infile.gff [ -o outfolder ]
agat_sp_separate_by_record_type.pl --help

OPTIONS

• -g, --gff or -ref

  Input GTF/GFF file.

• -o or --output

  Output folder. If no output folder provided, the default name will be <split_result>.

• -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 you the possibility to use your own AGAT config file (located elsewhere or named differently).

• -h or --help

  Display this helpful text.