General Information
| Description | A tool to identify common background presence in PAR-CLIP datasets |
| Homepage | https://github.com/phrh/BackCLIP |
Publications
BackCLIP: a tool to identify common background presence in PAR-CLIP datasets
Motivation
: PAR-CLIP, a CLIP-seq protocol, derives a transcriptome wide set of binding sites for RNA-binding proteins. Even though the protocol uses stringent washing to remove experimental noise, some of it remains. A recent study measured three sets of non-specific RNA backgrounds which are present in several PAR-CLIP datasets. However, a tool to identify the presence of common background in PAR-CLIP datasets is not yet available.
Results
: We used the measured sets of non-specific RNA backgrounds to build a common background set. Each element from the common background set has a score that reflects its presence in several PAR-CLIP datasets. We present a tool that uses this score to identify the amount of common backgrounds present in a PAR-CLIP dataset, and we provide the user the option to use or remove it. We used the proposed strategy in 30 PAR-CLIP datasets from nine proteins. It is possible to identify the presence of common backgrounds in a dataset and identify differences in datasets for the same protein. This method is the first step in the process of completely removing such backgrounds.
Availability
: The tool was implemented in python. The common background set and the supplementary data are available at https://github.com/phrh/BackCLIP.
Contact
: phreyes@gmail.com
Supplementary information:
Supplementary data are available at Bioinformatics online.
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