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

http://rpubs.com/chapmandu2/171024

Thanks also to Martin for help with ShortRead.