How to make paired-end sequencing multi-mapping reads have only the optimal two reads
l'm a starter,and I want to use a python script， but it can only identify matching reads,so how to filter out the multi-map read so that only the optimal unique mapping is retained？
thank you for your reply.
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minghuiguo448 •
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Hi,
Are you thinking about Generating consensus sequence from bam file?
Thanks for your answer.
But I don’t mean it, I mean how to keep only the optimal solution in the multi-map read？