Hello. I'm studding about RNASeq and specifically about differential expression techniques/pipelines. As anyone knows, the first step is to evaluate and filter the raw data. Actually there are tons of tools and papers evaluate them out there for this step. Here is a list of them in wikipedia. As also and some papers describing them. Paper 1, Paper 2.
The question is, which one to choose? Which one is the most used tool for that step using Illumina data?
Any idea or hint will be welcome