Processed data and analysis results for 104 RBPs

This repository makes available the processed data and the results of our SURF paper. 

The paper presents the Statistical Utility for RBP Functions (SURF) for integrative analysis of RNA-seq and CLIP-seq data. The goal of SURF is to identify alternative splicing (AS), alternative transcription initiation (ATI), and alternative polyadenylation (APA) events regulated by individual RBPs and elucidate protein-RNA interactions governing these events. We applied the SURF pipeline to analyze 104 RBP data sets (from ENCODE) and performed downstream analysis. Check out the browsable results from this shiny app!

The current repository includes:

• meme.326.input.zip -- input of 326 MEME runs on SURF-inferred location features
• meme.326.output.zip -- output of 326 MEME runs on SURF-inferred location features
• surf_inferred_feature.gtf -- SURF-inferred location features for 52 RBPs
• gencode.v24.annotation.filtered.gtf -- filtered genome annotation used for ENCODE data analysis
• Homo_sapiens.GRCh37.71.primary_assembly.protein_coding.gtf --  genome annotation used for simulation study
• simulation_truth.txt -- truth parameters used for RNA-seq simulation
• [RBP].results.rds -- SURF output (each an R object) for 104 RNA-binding proteins ([RBP] the protein name). 

For reproducing the results, the source code is available at DOI: 10.5281/zenodo.3779853.