FeatureCounts tool

Question

[Vikram]

Can we use a annotation file in GFF3 format in FeatureCounts tool ?

Answer 1

[Istvan Albert]

yep, just make sure to select for the correct attribute field that represents the hierarchy that connects exons to transcripts, most likely Parent

you may also need to remove lines that don't have the Parent field filled in, featurecounts will fail even if in the end does not use that particular line, it first it checks that every line has Parent, and only in the next step selects for features ... it is very annoying indeed