Hello everyone,
I've been having doubts about running each sample as a condition to get the FPKM trancking file as a table with all of the results and not the condesed one for each condition. Is is possible? Can it generate errors?
Thanks.
Hello,
You want to compare two samples from the same condition as individual conditions? Cuffdiff does not inherently know where the data is from so I wouldn't expect true errors.
This could be used as a test of sorts, a way of understanding more about the contents of each sample. Just be aware that this is a test and the differential expression results will be none to very small between two samples from the same condition for a reasonably "good" dataset.
Best, Jen, Galaxy team
Well I want to get a condensed FPKM table with each sample on it, thats why I want to run the samples separetaly. I'll run cuffdiff with each condition for the differential expressed genes too.
