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Old 07-07-2010, 04:16 PM   #1
noe
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Location: georgia

Join Date: Jul 2010
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Default Differential expression

Hello,

I d like to test differential expression between two conditions (i.e. treatment vs control, without replicates) but taken into account isoforms. So, if I want to use DESeq, my question is how to obtain the raw counts from cufflinks and at the same time deal with the uncertainty in the assignment of reads to transcripts.
Thanks,
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