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Old 06-21-2014, 12:22 PM   #1
Junior Member
Location: Utrecht

Join Date: Sep 2013
Posts: 9
Question Some chromosomes missing in bwa-output


I have fasta-files, resulting from a de novo assembly. When I map pe-reads to these fastas with bwa-mem (default options), it does not output all the fasta-entries: when looking at the bam-file and extracting the third column, not all fasta-ids can be found....

Is this because bwa-mem with default options does not output non-convered chromosomes? Or is there something else?

Many, many thanks!
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Old 06-21-2014, 01:01 PM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Are they all in the header?
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bwa 0.7.9, bwa mem, missing chromosomes, paired end mapping

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