These git submodules contain scripts and code associated with the manuscript "J. van Arensbergen et al: Systematic identification of human SNPs affecting regulatory element activity."
The 3 submodules are:
- SuRE-variants-pipeline: a pipeline for processing the raw sequencing data; fastq files for iPCR and cDNA samples are processed to generate:
- SuRE-counts tables (tabular data with SuRE-fragments and associated (SNP) annotation
- Bigwig tracks with genome-wide SuRE-signal profiles
- SuRE-raQTL-scripts: a collection of scripts to generate the raQTLs from the SuRE-count tables
- SuRE-figure-scripts: a collection of scripts used to generate some of the figures in the manuscript