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Those aren't raw counts, they're estimated raw counts.
Hint: don't try to coerce cufflinks data into DESeq.
Hint: don't try to coerce cufflinks data into DESeq.
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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?Comment
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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.Comment
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