I have RNA-Seq data from an experiment with multiple strains and conditions and wanted to clarify the correct setup for DEG using the tuxedo pipeline.
The experiment is looking at two C. elegans strains: wild-type and mutant, both water treated or drug treated, and triplicate for each, so 12 samples total (2 x 2 x 3). What I have done:
- I ran tophat for each sample, and then cufflinks separately for each sample.
- To compare drug treatment to water treatment, I cuffmerged all cufflinks files from the wild-type strain and then ran cuffdiff from that output. I did the same process for the mutant strain.
- This results in DEG for drug to water treatment in each strain separately, but I also want a comparison between strains. What would be the correct way of comparing the effect of drug treatment between the wild-type and mutant strain?
Thanks for the help, much appreciated!