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Old 06-18-2010, 06:49 AM   #2
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Location: Kansas City

Join Date: Mar 2008
Posts: 197

If you're comparing two organs, there's probably no control, but just liver vs. kidney or vice versa.

First you'll need to align the sequences to a genome (bowtie, bwa, or tophat if you want a spliced alignment). Then you may want to get either RPKMs or count data (cufflinks, bedtools coverageBed) with which you can use something to calculate differentially expressed genes (DEseq, DEGseq, edgeR).

I doubt it's a mundane task to very many people at this point, It's still pretty new and complicated to most people...
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