Thread: DESeq problems
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Old 08-05-2013, 04:44 AM   #18
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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The validity of the statistical model used by DESeq depends on its input being integer read counts directly from individual samples. Trying to use anything else will just produce unreliable results.

So yes, use htseq-count to generate your count matrix.
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