Question: how specify feature type in featureCounts
gravatar for lkianmehr
5 months ago by
lkianmehr30 wrote:


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

featurecounts • 434 views
ADD COMMENTlink modified 5 months ago by Macspider2.8k • written 5 months ago by lkianmehr30
gravatar for Macspider
5 months ago by
Vienna - BOKU
Macspider2.8k wrote:

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:

ADD COMMENTlink written 5 months ago by Macspider2.8k
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