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Old 10-17-2012, 04:52 AM   #1
tamari
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Location: Israel

Join Date: Oct 2012
Posts: 12
Red face DESeq and technical replicates

Hi,

I am working on RNA-seq data and I have few biological replicates and one technical replicate. From the DESeq manual I understood that I should just pool the counts from the technical replicates and treat it as one biological replicate. But I would like to preform some kind of test before I proceed with the DE analysis to check that the technical variation is not significant between the lanes.

I saw somewhere that it is possible to use scvplot to see that the technical noise is negligible relatively to shot noise but this option was removed from the latest DESeq version.

My question is, what are the alternatives to the scvplot or what is the best test to do in order to measure the technical reproducibility? Is is expression correlation?

Thanks,
tamari
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