Protocol to process crosslinking and immunoprecipitation data into annotated binding sites.
Shuhao Xu, Grady G Nguyen, Jack T Naritomi, Hema M Kopalle, Brian A Yee, Katherine L Rothamel, Evan A Boyle, Gene W Yeo
STAR protocols · 2024 · Vol. 5 (2) · pp. 103040
Abstract
Here, we present a protocol for using Skipper, a pipeline designed to process crosslinking and immunoprecipitation (CLIP) data into annotated binding sites. We describe steps for partitioning annotated transcript regions and fitting data to a beta-binomial model to call windows of enriched binding. From raw CLIP data, we detail how users can map reproducible RNA-binding sites to call enriched windows and perform downstream analysis. This protocol supports optional customizations for different use cases. For complete details on the use and execution of this protocol, please refer to Boyle et al.<sup>1</sup>.
Potentially related datasets 3
These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.
| Accession | Source | Title |
|---|---|---|
| ENCSR425FOI | ENCSR · ENCODE | No title in the index |
| ENCSR922QVQ | ENCSR · ENCODE | No title in the index |
| ENCFF269URO | ENCFF · ENCODE | No title in the index |
Funding 5 grants
| Grant | Funder |
|---|---|
| U24 HG009889 | NHGRI NIH HHS (United States) |
| R01 HG004659 | NHGRI NIH HHS (United States) |
| T32 CA067754 | NCI NIH HHS (United States) |
| U41 HG009889 | NHGRI NIH HHS (United States) |
| R01 CA273432 | NCI NIH HHS (United States) |