Count reads for gene with coordinates(collapsed exons)?

Question

[Tonkatsu]

How would I go about counting the number of reads falling into a specific gene by providing a list of coordinates? (I have heard about it is better to give coordinates of collapsed exons but I am not sure exactly how to do so)?

Answer 1

[ATpoint]

See featureCounts, it accepts custom SAF (see their docs) files with any coordinates you want and then quantifies over these intervals. It is part of subread:

http://subread.sourceforge.net/