An example RNA-Seq Quality Control and Analysis Workflow

I found the slides below on the education page from Bioinformatics & Research Computing at the Whitehead Institute. The first set (PDF) gives an overview of the methods and software available for quality assessment of microarray and RNA-seq experiments using the FastX toolkit and FastQC.



The second set (PDF)  gives an example RNA-seq workflow using TopHat, SAMtools, Python/HTseq, and R/DEseq.



If you're doing any RNA-seq work these are both really nice resources to help you get a command-line based analysis workflow up and running (if you're not using Galaxy for RNA-seq).