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?
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:
No magic here.