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Old 07-13-2010, 09:50 AM   #4
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Location: NYC

Join Date: Nov 2008
Posts: 4

OK, that was a very helpful idea to work with the index of just one chromosome. That worked fine. So I guess my problem is really about how do I index an entire genome of chromosome *.fa files? (i.e. the Mouse mm9 genome from UCSC); or once indexed, how do I point to all of them as a database for the 'bwa aln' command?

I did this by running the 'bwa index' command inside of a 'foreach' loop for each of my *.fa files. I got a lot of index files (.pac, .rpac, etc), but perhaps this is the source of my segmentation fault error.
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