An example RNA-Seq Quality Control and Analysis Workflow

December 6, 2011
By

(This article was first published on Getting Genetics Done, and kindly contributed to R-bloggers)

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).

To leave a comment for the author, please follow the link and comment on his blog: Getting Genetics Done.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...



If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.