Bioinformatics services- ChIP-seq

Chromatin immunoprecipitation sequencing (ChIP-seq) is used to identify DNA-protein interactions and study chromatin modifications. This technique helps to uncover regulatory regions of the genome, such as promoters, enhancers, and other transcription factor binding sites.

Pipeline Overview

1. Demultiplexing: Sorting reads based on sample-specific barcodes.
2. Quality Control (QC): Assessing the quality of raw data to detect issues like adapter contamination and low-quality reads using FastQC.
3. Mapping: Aligning the reads to a reference genome
4. Peak Calling: Identifying regions of the genome that show enriched binding signals, typically using tools like MACS2.
5. Peak Annotation: Annotating identified peaks with nearby genes or regulatory regions.
6. Differential Peak Detection [optional]: Identifying peaks that differ between experimental conditions.
7. Visualization: Creating genome-wide views of peak regions and visualizing enrichment profiles using tools like IGV.

Expected Result Output

1. Main Results File: A .bed or .narrowPeak file containing the identified peaks and their genomic coordinates.
2. Additional Results:
   • Differential Peak Analysis Output [optional]: A list of peaks showing significant differences between conditions, along with statistical values like fold change and p-value.
   • Heatmap: Heatmap of ChIP-Seq peaks binding to TSS (Transcription Start Site) regions.
   • Genomic Annotations Pie Chart – Genomic annotations of regions statistically enriched in ChIP-Seq data, including location distribution within the genome.
   • PCA Plot: To check the variability between samples and detect potential outliers.
   • IGV View: A snapshot showing binding regions or peak enrichment across the genome.