I have rna-seq data from paired samples and want to do isoform-level differential expression.
My understanding is that is not possible to explicitly specify paired design in cuffdiff, so I considered the option of using the isoforms.read_group_tracking file and extract the 'raw_frags' column, which I *think* corresponds to counts. Then use this as input in edgeR where I can specify paired-sample design.
Does this sound sensible?
If not, my question is: which package can I use to do isoform-level DE which takes into consideration paired-sample designs.