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Old 09-07-2011, 05:59 AM   #1
Location: Finland

Join Date: Jun 2011
Posts: 24
Default Index for bfast with Arabidopsis


I have an RNA-Seq data set from Arabidopsis (SOLiD, 50+35bp PE) which I would like to try to align with bfast (or bfast+bwa, I guess). I was hoping for some help with building the index -- I don't really know what mask, key size or key width to use. I've had a look at the bfast book and the paper, but I'm still at a bit of a loss. My next step is to read the supplement to the paper in the hope of understanding things well enough to answer these questions, but it occurred to me that someone might been through this before and might be willing to help out.

Does anybody know what indexes would be good to use with A. thaliana? Or maybe some quick pointers to help me figure it out?
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