...
First, below is a snapshot of what a RIP-Seq "peak" region might look like. This data was from a well-known PRC2 RIP-Seq dataset included in the same paper that the RIP-Seq schematic diagram was taken from:
Here, the reads were filtered to remove all duplicates (i.e. reads aligning to the exact same genomic coordinates). This is a strategy sometimes used to counteract the problem of PCR artifacts, particularly when quantitative measurements are less important than whether the protein and RNA are associated (a binary classification problem). Thus, each 'read' as it is depicted above could represent several actual reads from the raw data. The reads occur mostly in exons, and are distributed over the length of Xist, a known binding partner of PRC2.
In a CLIP-seq experiment, this view would look quite different.
