How to treat with high mismatch reads in whole genome studies?
Hi all friends
I have whole genome project, during this alignment with human genome I faced with a big challenge, how to treat with un-mapped reads which have high mismatches for example 20-30 mismatches in a read. Because, usually aligners discard them and save them in an un-mapped reads file.
But my questions is, Is there any way to do more work on them or I have to ignore them?
Many thanks
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