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Old 07-13-2010, 08:17 AM   #2
nickloman
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Location: Birmingham, UK

Join Date: Jul 2009
Posts: 356
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Isn't BWA called as follows:

bwa aln <database> <FASTQ file>

a la

http://bio-bwa.sourceforge.net/bwa.shtml

Edit: Actually I can see you did that already. Did you run bwa index on the mouse database first?
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