agat_sp_flag_short_introns.pl
DESCRIPTION
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
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.