Hey all, I couldn't find anything using the search function, so I'll just ask here. If this is the wrong spot, please feel free to move, or tell me where it should be posted.
Question is this: I have 2 varieties of rice, treated at 3 time points, and untreated at time=0. 3 bio reps for each "treatment". I ran cufflinks, and got .gtf files for each treatment. then used cuffmerge to put all 24 treatments into a single "super.gtf". Can I use this super.gtf in cuffdiff if I am only going to compare two samples? Or should I use cuffmerge to merge those two samples' gtf files, and use that specific combined.gtf in my cuffdiff command? It would be nice if I could just use the "super.gtf" for all my comparisons.
Thanks!
Question is this: I have 2 varieties of rice, treated at 3 time points, and untreated at time=0. 3 bio reps for each "treatment". I ran cufflinks, and got .gtf files for each treatment. then used cuffmerge to put all 24 treatments into a single "super.gtf". Can I use this super.gtf in cuffdiff if I am only going to compare two samples? Or should I use cuffmerge to merge those two samples' gtf files, and use that specific combined.gtf in my cuffdiff command? It would be nice if I could just use the "super.gtf" for all my comparisons.
Thanks!
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