featureCounts for WGS instead of RNA-seq

Question

[BioDH]

Hello all,

I have done whole genome sequencing and aligned reads on a reference genome.

I have some bam files.

I want to get the number of reads mapped to sepecific regions defined in a gff3 files.

I have used featureCounts for RNA-seq but not for WGS.

Can I use it to get read counts? Which library type do I need to specify?

FYI, I did paired-end seq.

If it is not recommended, any suggestions?

Answer 1

[Martombo]

featureCounts is going to count mapped reads in genomic intervals on whatever kind of data you feed it as input, so it can work on WGS. Of course you'll have to adjust the program options for it to make sense, depending on what is your aim. Be careful, for example, of the distinction between feature and meta-feature counting (gene level), which is the default for featureCounts, the attribute / feature type of the annotation file that you're using and all the options for read filtering and interval overlap. I'm not sure what you are referring to with library type though.

[ATpoint]

Library type would be accounting for stranded libraries in RNA-seq which does not apply for WGS, so you can just leave that option empty/do not set anything. I would simply make a SAF file (see featureCounts manual) of the features you want to count, and then just do:

featureCounts -a your.saf -F SAF -o out.counts your.bam

No magic here.