@article{Uhl_Houwaart_Corrado-Compu_Analy_CLIP-2017,
author = {Uhl, Michael and Houwaart, Torsten and Corrado, Gianluca 
          and Wright, Patrick R. and Backofen, Rolf},
title = {Computational analysis of {CLIP}-seq data},
journal = {Methods},
year = {2017},
doi = {10.1016/j.ymeth.2017.02.006},
volume = {118-119},
user = {wrightp},
pmid = {28254606},
pages = {60-72},
number = {},
issn = {1046-2023},
abstract = {CLIP-seq experiments are currently the most important means 
            for determining the binding sites of RNA binding proteins on 
            a genome-wide level. The computational analysis can be 
            divided into three steps. In the first pre-processing stage, 
            raw reads have to be trimmed and mapped to the genome. This 
            step has to be specifically adapted for each CLIP-seq 
            protocol. The next step is peak calling, which is required 
            to remove unspecific signals and to determine bona fide 
            protein binding sites on target RNAs. Here, both 
            protocol-specific approaches as well as generic peak callers 
            are available. Despite some peak callers being more widely 
            used, each peak caller has its specific assets and 
            drawbacks, and it might be advantageous to compare the 
            results of several methods. Although peak calling is often 
            the final step in many CLIP-seq publications, an important 
            follow-up task is the determination of binding models from 
            CLIP-seq data. This is central because CLIP-seq experiments 
            are highly dependent on the transcriptional state of the 
            cell in which the experiment was performed. Thus, relying 
            solely on binding sites determined by CLIP-seq from 
            different cells or conditions can lead to a high false 
            negative rate. This shortcoming can, however, be 
            circumvented by applying models that predict additional 
            putative binding sites.}
}