Data for: iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites
Accompanying files Supplementary Data 1: Bash code for all steps from raw reads until peak calling. This file provides the bash code for basic read processing, conversion into crosslink events and peak calling as described in Chapters 3-5.1. Details on the input files, preset variables and external tools required to run this code are listed in Chapters 2.1 and 3.1. Supplementary Data 2: R code for postprocessing of PureCLIP output. This file provides the R code to postprocess the output of PureCLIP peak calling as described in Chapter 5.2. Running this code requires a bed file with ’crosslink sites’ output by PureCLIP (PureCLIP.crosslink_sites_short.bed) and bw files with crosslink events (sampleX.strand.bw). The code to obtain these files is described in Supplementary Data 1. Supplementary Data 3: R code for reproducibility and downstream analysis. This file provides the R code to reproducibility analyses and assignment of genes and transcript regions as described in Chapters 6.1 and 6.2. Running this code requires a bed file with binding sites (e.g. curated PureCLIP output, see Chapter 5), a gtf file with gene/transcript annotations, and bw files with crosslink events in the individual replicates (sampleX.strand.bw, see Chapter4).