I'm faceting a vital dilemma and I'd need some advices, please. Up to now, I've processed some samples according a 3`-based RNAseq protocol... but currently I have the option to process the new ones with a full-length protocol (that will give me, theoretically, more information).
I guess, according the paper I attached, it's not feasible (or correct) to directly compare the final matrix counts... so I should realign my BAMs to a custom reference containing only the 3' ends for each gene. Do you know if there's already any way to do this? Or there is any study that have already done this? (I've found nothing).
Beyond technical aspects, what's your view about using two different (very different) protocols? Maybe could be better to use the same for the entire project?
Thanks a a lot. Bests.