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robinweide 06-21-2014 11:22 AM

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!

dpryan 06-21-2014 12:01 PM

Are they all in the header?

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