We've just been trialling the Lexogen Quantseq 3'-UTR RNAseq protocol and I thought I'd share the write-up I put together in case anyone else finds it useful. I really valued being able to do this all in Bioconductor since I wasn't having to swap environments all the time to use different tools and work out what was going on. The techniques used include:
- ShortRead to manipulate, filter and quality check reads
- RSubread to do the alignment
- RSubread to do the feature counting
- ensembldb to conveniently access annotation
- ggplot2 and the cowplot extension for doing nice plots
Thanks also to Martin for help with ShortRead.