CHAMPAGNE v0.1.0

This release implements nearly all QC steps from the original CCBR pipeliner chip-seq workflow.

Quality control steps implemented for single-end reads

• Trim raw reads, FastQC on raw and trimmed reads, and FastQ Screen on trimmed reads.
• Exclude reads that align to blacklist regions, align remaining reads to the reference genome, and deduplicate.
• Preseq on aligned reads.
• Phantompeakqualtools on aligned and deduplicated reads.
• Process reads with deepTools: bam coverage to generate bigwigs for each sample, summarize all bigwigs, and compute matrices relative to TSSs and scaled to metagene regions.
• Generate plots with deepTools: PCA, profile, heatmap, spearman correlation, and fingerprint plots.
• Summarize all quality control steps in a MultiQC report.
• Input-normalize ChIP fragments for the next stage of the pipeline.