agat_sp_list_short_introns.pl#
DESCRIPTION#
The script aims to list all the introns inferior to a certain size. Introns are calculated on the fly from exons. (intron feature will not be used).
SYNOPSIS#
agat_sp_list_short_introns.pl --gff infile [ --out outFile ]
agat_sp_list_short_introns.pl --help
OPTIONS#
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--gff, -f, --ref or -reffile
Input GTF/GFF file.
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--size or -s
Minimum intron size accepted in nucleotide. All introns under this size will be reported. Default value = 10.
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--out, --output or -o
Output gff3 file where the gene incriminated will be write.
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-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).
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--help or -h
Display this helpful text.