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Objectives

In this exercise, you will use a recently developed R package called RIPSeeker to identify binding regions in a small CLIP-seq dataset.

Primary Data

Ameyar-zazoua M, Rachez C, Souidi M, et al. Argonaute proteins couple chromatin silencing to alternative splicing. Nat Struct Mol Biol. 2012;19(10):998-1004.

RIPSeeker

RIPSeeker is a Bioconductor R package, and we are going to run the job using the "Rscript" utility using the script and commands file that exist in the directory you just staged.  Check out the "ripseeker_script.R" file.

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The important file is RIPregions.gff3, which is a coordinate file of the regions predicted to be enriched in the IP.  Because of the extremely slimmed-down dataset we used, there is only one peak, but this pipeline (with more reads that are actually real) would produce a file that is more interesting.

Alternatives

We could have added these lines to the ripseeker_script.R file:

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