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Tutorial: Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
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gravatar for phil.chapman
15 months ago by
phil.chapman120
United Kingdom
phil.chapman120 wrote:

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.

 

 

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