how specify feature type in featureCounts

Question

[lkianmehr]

Hello,

I would appreciate if let me know how is better to specify feature type of featureCounts. actually I am not sure about that, because by default is exon, but I want to count genes and transcripts (according to 3rd column in GTF file) on sam files, so I got mixed up I have to define feature type as gene (meta feature) or exon or what else? and what does meta features mean? it means the aggregate of all features or just based on gene count?

does anybody have a suggestion?

thanks in advance

Answer 1

[Matteo Schiavinato]

Your feature is defined by the 3rd column of your GTF/GFF file. As you said, the default is exon, but you can change it to any of the features that you have in your GTF file.

cut -f 3 <GTF_file> | sort | uniq will give you all the possible features you can use.

Regardless of the feature you choose, featureCounts will go through the SAM file and count +1 everytime some SAM record overlaps one of the feature-types in the GTF.

All the examples are at: http://bioinf.wehi.edu.au/featureCounts/