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In this exercise, you will use a recently developed R package called RIPSeeker to identify binding regions in a small CLIP-seq dataset. This dataset has been MASSIVELY down-sampled, since otherwise staging and processing the data would be difficult. As a result, this dataset should produce only ONE peak in the entire human genome. Let's try to find it!
Primary Data
This data is derived from an Ago2 CLIP-seq experiment (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.), and is located at:
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$BI/rnaseq_course/ripseq_exercises/CLIP |
Stage it in your Scratch area in
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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