agat_sp_statistics.pl

DESCRIPTION

The script provides exhaustive statitics of a gft/gff file. /!\ If you have isoforms in your file, even if correct, some values calculated might sounds incoherent: e.g total length mRNA can be superior than the genome size. Because all isoforms lengh are aditionned... It is why by deafault we always compute the statistics twice when there are isoforms, once with the isoforms, once wihtout (In that case we keep the longest isoform per locus).

SYNOPSIS

agat_sp_statistics.pl --gff file.gff  [ -o outfile ]
agat_sp_statistics.pl --help

OPTIONS

• --gff or -i

  Input GTF/GFF file.

• --gs, -f or -g

  This option inform about the genome size in oder to compute more statistics. You can give the size in Nucleotide or directly the fasta file.

• -d or -p

  When this option is used, an histogram of distribution of the features will be printed in pdf files. (d means distribution, p means plot).

• -v or --verbose

  Verbose option. To modify verbosity. Default is 1. 0 is quiet, 2 and 3 are increasing verbosity.

• --output or -o

  File where will be written the result. If no output file is specified, the output will be written to STDOUT.

• -h or --help

  Display this helpful text.