Question

bwa samse multiple hits

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9.1 years ago

schelarina ▴ 50

Can someone please explain me what does really mean that "Repetitive hits will be randomly chosen" in BWA samse?

the manual does not really specify

thanks

RNA-Seq alignment • 1.8k views

ADD COMMENT • link updated 9.1 years ago by Pierre Lindenbaum 164k • written 9.1 years ago by schelarina ▴ 50

Ram · Answer 1 · 2015-10-29

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9.1 years ago

Pierre Lindenbaum 164k

if a read maps multiple positions (hit) in the genome, only one position will be used.

ADD COMMENT • link 9.1 years ago by Pierre Lindenbaum 164k

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ok thanks. Do you know how to tell bwa to do not randomly choose and to map all the multiple hit reads?

ADD REPLY • link updated 5.0 years ago by Ram 44k • written 9.1 years ago by schelarina ▴ 50