Hello, apologies if this is a dumb question, I am relatively new to RNAseq. I have processed 9 samples through TopHat and Cufflinks, but as none of my samples have replicates I won't be using Cuffdiff to test for differential expression. My understanding is that my best option is to compare raw gene expression values through FPKM output from Cufflinks. I want to compare gene FPKM values across two Cufflinks gene expression files, and I am unsure as to how I can do that, any suggestions? Thanks in advance for any help, I'd really appreciate it!
Review the tool Cuffcompare to discover what is in common and what is not between the experiments.
From there, specific transcript sets can be extracted by using a Join on the common transcript/gene identifier. FPKM between experiments will be placed on the same line in the output, making it easier for statistics/graphs to be generated.
If you are not using reference annotation, a less precise comparison would be done by examining transcripts with overlapping genome footprints. Using tools in the group Operate on Genomic Intervals is one to perform a merge between experiments where only overlapping coordinates are in common.
Hopefully this helps, Jen, Galaxy team