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Old 02-04-2014, 07:49 AM   #1
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Location: Pennsylvania

Join Date: Oct 2012
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Default RNAseq and qPCR don't agree, but only some genes

I've done RNAseq on bacterial samples for gene expression studies over a time course, and have been validating some of the results via qPCR, using the same RNA samples as we sent for sequencing. Most of the qPCR results correlate well with the RNAseq results.

For only a handful of the genes I've tested, however, and at only one of the timepoints, my qPCR results for fold-change are much lower than those from the RNAseq analysis. This seems to be biologically relevant, as all the genes so far that follow this pattern encode members of a particular family of proteins. However, how do I know which set of data has the correct fold-change?
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