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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)

The script output a folder containing a report of number of different cases as well as a file per case type listing per line the gene feature's ID involved in each case.

SYNOPSIS#

agat_sp_compare_two_annotations.pl --gff1 infile1.gff -gff2 infile2.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 folder. It contains a report that resume the type and number of cases, as well as a file per case type containing one case per line with the list of gene feature's ID (or other type of feature level1) from file1 then file2 separated by a |.

  • -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.