agat_sq_list_attributes.pl

DESCRIPTION

The script take a gff3 file as input. - The script give information about attribute tags used within you file.

SYNOPSIS

agat_sq_list_attributes.pl -gff file.gff -p level2,cds,exon [ -o outfile ]
agat_sq_list_attributes.pl --help

OPTIONS

• --gff or -f

  Input GTF/GFF file.

• -p, -t or -l

  primary tag option, case insensitive, list. Allow to specied the feature types that will be handled. You can specified a specific feature by given its primary tag name (column 3) as: cds, Gene, MrNa You can specify directly all the feature of a particular level: level2=mRNA,ncRNA,tRNA,etc level3=CDS,exon,UTR,etc By default all feature are taking in account. fill the option by the value "all" will have the same behaviour.

• -o , --output , --out or --outfile

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

• -h or --help

  Display this helpful text.