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06-21-2014, 12:22 PM
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#1 |
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Junior Member
Location: Utrecht Join Date: Sep 2013
Posts: 9
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Some chromosomes missing in bwa-output
Hello!
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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06-21-2014, 01:01 PM
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#2 |
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Devon Ryan
Location: Freiburg, Germany Join Date: Jul 2011
Posts: 3,480
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Are they all in the header?
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| Tags |
| bwa 0.7.9, bwa mem, missing chromosomes, paired end mapping |
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