agat_sp_compare_two_annotations.pl

DESCRIPTION

The script aims to compare two annotation of the same assembly. It provided information about split/fusion of genes between the two annotations. The most common case are: 1 => 0 ( gene uniq to file1) 0 => 1 ( gene uniq to file2) 1 => 1 ( 1 gene from file 1 overlaps only 1 gene from file2) 1 => <many> ( 1 gene from file 1 overlaps <many> genes from file2) => split case (with file 1 as reference) <many> => 1 ( <many> genes from file 1 overlap only 1 gene from file2) => fusion case (with file 1 as reference)

Then you can get more complex cases: <many> => <many> (<many> genes from file 1 overlap <many> genes from file2)

SYNOPSIS

agat_sp_compare_two_annotations.pl -gff1 infile.gff [ -o outfile ]
agat_sp_compare_two_annotations.pl --help

OPTIONS

  • -gff1

    Input GTF/GFF file1.

  • -gff2

    Input GTF/GFF file2.

  • -o , --output , --out or --outfile

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

  • -v

    Verbose option, make it easier to follow what is going on for debugging purpose.

  • -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.