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Old 01-29-2019, 12:39 PM   #4
seb567
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Location: Québec, Canada

Join Date: Jul 2008
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If you'are using "bwa sampe" for aligning, the documentation says:

Quote:
Generate alignments in the SAM format given paired-end reads. Repetitive read pairs will be placed randomly.
I don't know if it is the case with "bwa mem" or with "bwa aln".
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