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Old 01-31-2020, 01:54 AM   #2
fkrueger
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Location: Cambridge, UK

Join Date: Sep 2009
Posts: 625
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Hi Hedi,

Every alignment that is reported by Bismark are unique hits (ambiguosly aligning reads are discarded, and not-aligning reads - well - don't align at all). So you can simply look at the aligned read length distribution using your program of choice. It would only be 2 clicks in SeqMonk for example. As a general rule though, longer reads tend to align better.

40% mapping efficiency doesn't sound great to be honest. Which organisma are you working with, and did you perform appropriate adapter/quality trimming etc?
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