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agat_sp_flag_short_introns.pl#

DESCRIPTION#

Looking at exon features the script flags each feature of a record with the <short_intron> attribute if it contains an intron with a size below the <--intron_size> threshold (10bp by default). The value of this attribute will be the size of the shortest intron found under the threshold.

SYNOPSIS#

agat_sp_flag_short_introns.pl --gff infile --out outfile
agat_sp_flag_short_introns.pl --help

OPTIONS#

  • --gff, -f, --ref or -reffile

    Input GTF/GFF file.

  • --intron_size or -i

    Minimum intron size, default 10. All genes with an intron < of this size will be flagged with the pseudo attribute (the value will be the size of the smallest intron found within the incriminated gene)

  • --out, --output or -o

    Output gff3 file where the result will be printed.

  • -v

    Bolean. Verbose 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).

  • --help or -h

    Display this helpful text.