CLIP-Seq protocols such as PAR-CLIP, HITS-CLIP or iCLIP allow a genome-wide 
analysis of protein-RNA interactions. For the processing of the resulting short 
read data, various tools are utilized. Some of these tools were specifically 
developed for CLIP-Seq data, whereas others were designed for the analysis of 
RNA-Seq data. To this date, however, it has not been assessed which of the 
available tools are most appropriate for the analysis of CLIP-Seq data. This is 
because an experimental gold standard dataset on which methods can be accessed 
and compared, is still not available. To address this lack of a gold-standard 
dataset, we here present Cseq-Simulator, a simulator for PAR-CLIP, HITS-CLIP and 
iCLIP-data. This simulator can be applied to generate realistic datasets that 
can serve as surrogates for experimental gold standard dataset. In this work, we 
also show how Cseq-Simulator can be used to perform a comparison of steps of 
typical CLIP-Seq analysis pipelines, such as the read alignment or the peak 
calling. These comparisons show which tools are useful in different settings and 
also allow identifying pitfalls in the data analysis.