Hi, I am using the linux version of featureCounts, and I would like to count the number of reads in CDS, 5'UTR and 3'UTR. I was wondering if I should just count three times like:

featureCounts -t CDS -g gene_id -a $GTF -o counts.txt $BAM

featureCounts -t five_prime_UTR -g gene_id -a $GTF -o counts.txt $BAM

featureCounts -t three_prime_UTR -g gene_id -a $GTF -o counts.txt $BAM

Or is there a way to do all three together? Thanks!!!

Regarding questions related to featureCounts that is released as part of the SourceForge Subread package, please send your question to Google Subread group (https://groups.google.com/forum/#!forum/subread).

You cannot count reads to three different types of features at one time with your current GTF annotation file. However you can get around this by changing the names of the three feature types to the same name, for example you may rename all of them to 'CDS_or_5UTR_or_3UTR'. Then you can count reads to all the three types in one command:

featureCounts -t CDS_or_5UTR_or_3UTR -g gene_id -a $GTF -o counts.txt $BAM

But this might take more effort than simply summing up the counts you got from the three individual counting.