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bwa samse multiple hits

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
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by schelarina • schelarina

1 answer

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

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written by Pierre Lindenbaum Pierre Lindenbaum

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

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updated by Ram Ram • written by schelarina • schelarina

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