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.
...
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:
...