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williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments
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the meaning of "anti-over, anti-near, clean, known exon" in the output file #69

Closed genemine closed 4 years ago

genemine commented 4 years ago

Hi there, In the IRFinder output file, the introns are annotated with tags including anti-over, anti-near, clean, known exon. Can you please help explain what they mean exactly? Thanks.

dg520 commented 4 years ago

Hi @genemine ,

Each of these terms refers to whether an intronic region is a pure intron or if the region is overlapped with other features in the GTF annotation. You can check the script bin/util/IntronExclusion.pl in your IRFinder folder for the detailed definition of these terms if you are familiar. I listed a brief description below:
clean: a pure intron in the annotation
known-exon: the intronic region is contained by an annotated exon
anti-over: the intronic region overlaps with a gene on the antisense strand
anti-near: the intronic region has a nearby gene on the antisense strand, where 'nearby' means within 5000bp upstream and 1000bp downstream.

Best, Dadi