Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs

We present RCRUNCH, an end-to-end solution to CLIP data analysis for identification of binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze not only reads that map uniquely to the genome but also those that map to multiple genome locations or across splice boundaries and can consider various types of background in the estimation of read enrichment. By applying RCRUNCH to the eCLIP data from the ENCODE project, we have constructed a comprehensive and homogeneous resource of in-vivo-bound RBP sequence motifs. RCRUNCH automates the reproducible analysis of CLIP data, enabling studies of post-transcriptional control of gene expression.

Automated summary

We present RCRUNCH, an end-to-end solution for CLIP data analysis that identifies binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze reads that map uniquely to the genome as well as reads that map to multiple genome locations or across splice boundaries, considering various background types for read enrichment estimation. Applying RCRUNCH to eCLIP data from the ENCODE project, we have created a comprehensive and homogeneous resource of in-vivo-bound RBP sequence motifs. RCRUNCH automates reproducible analysis of CLIP data, facilitating studies on post-transcriptional control of gene expression.