RNA-Seq Analysis Survey

this was originally posted on the SEQanswers forum by bodhisattvax

I am looking to build a ‘standard’ RNA-seq data analysis pipeline for analysing differential gene and possibly transcript expression.

I am aware that there are a variety of tools out there for the various steps (alignment, counting, differential expression), each with their respective pros and cons, cheerleaders and dissers.

So I have created a (short) survey which I think could be useful to all of us, to try and see if we are moving towards some consensus about the preferred methodology for each of the steps.

The survey is at
I would be very grateful if you could fill it out : it should only take a few minutes of your time.

You may prefer to respond within this thread itself but being an optimistic soul, I’m hoping that I get so many responses that I will need to use the results analysis tools on survey monkey!

Of course, I will make the results available either here or on request.

Thanks in advance.