I have RNA-seq data on pre and post intervention. 24 patient samples pre, and then 24 patient samples after the intervention. I will be performing a cuffdiff analysis looking at difference between pre vs. post, but also at different phenotypes.
Should I use cuffmerge to merge just the pre gtf files, or should I put both the pre and post into the assemblies files together, knowing that the post samples are from the same patients (but post intervention).
Thanks for any insight.
Should I use cuffmerge to merge just the pre gtf files, or should I put both the pre and post into the assemblies files together, knowing that the post samples are from the same patients (but post intervention).
Thanks for any insight.
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