Although this question has been addressed before, I would like to bring it up again, as I would need it for a study and the state-of-the-art may have changed.
I am working with a reference genome and different clones. I have RNA-Seq data from these clones. I would like to do a DE transcript analysis, but also to determinate the sequence of certain already known transcripts in these clones (so I cannot merely extract the sequences using the reference genome).
Which would be the best way for addressing this?
I guess I could assembly the reads using Trinity, and obtain the sequence of these transcripts, while doing the DE analysis using the TopHat+Cufflinks Suite + DeSeq. Is this the most correct way to act, taking into account that I want this study for a paper? What would you do? Do you know of similar examples already done in previous papers? I have taken a look, but I have not been lucky.
Thank you for your time, and sorry for bothering you.