CHIPS

CHIPS processes chromatin profiling data from ChIP-seq, ATAC-seq, and DNase-seq to identify enriched genomic regions, compute quality metrics, and annotate regulatory elements for studies of gene regulation.

Key Features:

• Pipeline Architecture: Implemented in Snakemake to orchestrate reproducible workflow execution across processing steps.
• Data Flexibility: Accepts single- and paired-end sequencing data and can start from FASTQ or BAM files.
• Read Trimming and Mapping: Performs quality trimming of reads followed by mapping to a reference genome.
• Peak Calling: Identifies regions of enrichment from chromatin profiling experiments.
• Quality Control Metrics: Computes contamination profiles, polymerase chain reaction bottleneck coefficient, fraction of reads in peaks, percentage of peaks overlapping public DNaseI hypersensitivity sites, and conservation profiles of peaks.
• Peak Annotation: Assigns functional annotations to identified genomic regions.
• Motif Finding: Detects DNA sequence motifs within peak regions to infer potential transcription factor binding sites.
• Regulatory Potential Calculation: Quantifies the regulatory impact of peaks on gene expression across the genome.

Scientific Applications:

• Regulatory element identification: Detection and annotation of promoters, enhancers, and other regulatory regions from ChIP-seq, ATAC-seq, and DNase-seq data.
• Transcription factor and chromatin accessibility analysis: Characterization of transcription factor binding sites and open chromatin landscapes via peak calling and motif discovery.
• Disease mechanism investigation: Analysis of chromatin features and regulatory elements relevant to disease etiology.
• Developmental biology studies: Profiling chromatin changes and regulatory regions across developmental pathways.

Methodology:

Workflow execution with Snakemake; quality trimming of reads; mapping reads to a reference genome; peak calling; computation of contamination profiles, PCR bottleneck coefficient, fraction of reads in peaks, overlap with public DNaseI hypersensitivity sites, and conservation profiles; peak annotation, motif finding, and regulatory potential calculation.