Thread: DESeq problems
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Old 08-05-2013, 04:40 AM   #17
vd4mindia
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Location: Milan

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So, you saw that since these are estimated raw counts and they are coming from cufflinks which are infact considering noise for duplicate read counts as well. However for DESeq we donot consider the duplicate read counts right? For DESeq each counting unit is evidence of one sequencing read. So we should not consider this estimated raw count and rather generate the raw count using HT-Seq for my data and then use them for DESeq analysis? Is that what you want to mean?
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