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agat_sp_manage_introns.pl#

DESCRIPTION#

The script provides information about introns (longest, shortest size mean ...) using the statistic method, then plot all the intron size values to get an overview of the introns size distribution. It gives you as well the value of the longest intron after removing X percent(s) of the longest (removing potential biais / false positive).

SYNOPSIS#

agat_sp_manage_introns.pl --gff infile [--out outFile]
agat_sp_manage_introns.pl --help

OPTIONS#

  • --gff, -f, --ref or -reffile

    Input GTF/GFF file. You can use several input files by doing: -f file1 -f file2 -f file3

  • -w, --window, --break, --breaks or -b

    It the number of break used within the histogram plot. By default it's 1000. You can modify the value to get something more or less precise.

  • -x, --p

    Allows to modify the X values to calculate the percentage of the longest introns to remove. By default the value is 1 (We remove 1 percent of the longest).

  • --plot

    Allows to create an histogram in pdf of intron sizes distribution.

  • --out, --output or -o

    Output gff3 file where the gene incriminated will be write.

  • -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).

  • --help or -h

    Display this helpful text.