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Old 04-24-2012, 11:19 PM   #4
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Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438

So the next step would be to use a tool like Cufflinks to quantify expression of genes in terms of some annotation - typically a GTF file from ensemble or UCSC's table browser. That and make a bedGraph of your alignments so you can view them in the UCSC genome browser.
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