Hello, I was wondering what sort of parameters were used to calculate significance in Cuffdiff. I recently analyzed three replicates of RNA-seq data and successfully evaluated the differential transcripts between 2 conditions. However, with this most recent data set, I see a very large fold change in some transcripts, but none are deemed significant. What could be happening to make this happen? *My more recent run had data sets with much lower percentages of mapped reads (~5%). *My previous, successful run was using paired end alignments and this run is using single end.
All other parameters were kept the same.
I would appreciate any advice! Thanks, Mike