Dear all,

I want to do differential expression at **transcript level** using an RNA-seq dataset that consists of **paired samples** (patient 1 control/treatment, patient2 control/treatment, etc.).

I have not found methods other than Ballgown and DEXSeq that are able to handle paired designs. I have also tried the option of obtaining **transcript counts** and use them in edgeR. However I am concerned about the fact that edgeR is not particularly adapted to do analysis on transcript counts.

Does anyone has any advice on how to go on this problem? Or if there is a way to assess my results with the latter approach I described?

Many thanks,  
Maria
Perhaps not the solution you were looking for, but software like kallisto and Salmon (and others) generate estimates of raw counts per transcript. You could use those estimates in edgeR or DESeq2.