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Old 05-06-2012, 11:53 AM   #1
Location: germany

Join Date: Feb 2012
Posts: 15
Default Cuffdiff-- replicates

Hi everybody,

I have six samples for RNA-Seq. 3 WT and 3 mutants.

I think the amount of RNA used for each library construction might vary.

If people loaded a bit more RNA for one sample, there will be more reads in this sample.

As we know, for qPCR, we use some genes (GAPDH...) as internal control.

My question is how cuffidiff normalized this variation in the amount of RNA used for RNA-seq??

Looking forward to hearing from you.

guzhi100 is offline   Reply With Quote
Old 05-06-2012, 12:30 PM   #2
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Location: San Francisco, CA

Join Date: Feb 2011
Posts: 286

Its normalizing to the total number of reads in each sample and across all samples, I believe, so it shouldn't matter if some of the replicates have more total reads than others.
Wallysb01 is offline   Reply With Quote

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