Originally posted by ThePresident
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has the 'not primary alignment' flag set?
I'm also trying to simplify by excluding both mates if either is multi mapped
(i.e., has flag 256 set or has NH field set with something other than NH:i:1).
This should be extremely conservative in giving uniquely mapped reads.
I plan to run these through cufflinks, htseq-count, and featureCounts
to compare results.
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