Count reads for gene with coordinates(collapsed exons)?
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)?
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ATpoint
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Tonkatsu •
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Tonkatsu •
1 answer
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:
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