Tutorial:Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
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phil.chapman ▴ 150
@philchapman-8324
Last seen 4.9 years ago
United Kingdom

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.

 

 

shortread rsubread ensembldb Tutorial • 2.1k views
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Thanks a lot for sharing your workflow!

Just curious: the titles says "Analysis of Lexogen Quantseq Data: Part 1". Is there a "Part 2" anywhere?

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