Hi, I have to start working with RNA-Seq data and have worked previously with ChIP-Seq so I am familiar with mapping, coverage, visualizations and tools etc. Could you guys please tell me a simple workflow (published/unpublished) for the analysis of RNA-Seq data, analysing the gene expression between a wild type and knockout sample. I tried rseq, galaxy (which is good) and GENE-Counter, still I am not confident with my analyses and I get lost in the downstream analyses. Could you recommend a good review and pipeline to start with!!
Thanks a lot