The script flags the short introns with the attribute <pseudo>. Is is usefull to avoid ERROR when submiting the data to EBI. (Typical EBI error message: ********ERROR: Intron usually expected to be at least 10 nt long. Please check the accuracy)

SYNOPSIS --gff infile --out outfile --help


  • --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.