EPIGENOMICS 30 days · 6 modules · Online

ChIP-Seq Data Analysis Workshop (30-Day, Online)

Map protein-DNA interactions and histone modifications from raw sequencing reads to peaks, motifs and differential binding.

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About this workshop

ChIP-Seq shows where a protein, such as a transcription factor, or a chemical mark on histones sits along the genome. It answers questions like which genes a factor controls and how regulation changes between conditions. The signal is noisy, so good analysis depends on careful filtering, proper use of control samples and sensible peak calling. This workshop takes you through each stage: aligning reads, removing artefacts, calling peaks, linking them to nearby genes, discovering the DNA motifs the protein recognises and testing for differences in binding between conditions. You also learn to create signal tracks and profile plots for figures. The mini-project brings it together on a real dataset, so you leave able to analyse your own ChIP-Seq experiments independently.

Tools and pipelines you will use

This workshop emphasizes standard, open-source bioinformatics tools widely used in peer-reviewed genomics literature:

FastQC ↗Bowtie2 ↗Samtools ↗MACS3 ↗deepTools ↗MEME-ChIP ↗HOMER ↗ChIPseeker ↗DiffBind ↗

What you will learn

Module 1 Foundations
Week 1
Linux and command-line basics Navigate files, run programs and keep analyses organised.
Sequencing and ChIP-Seq concepts How the assay works and what the reads represent.
File formats FASTQ, BAM, BED and bigWig, and when each is used.
Read quality control Judge read quality and trim adapters and poor bases.
Module 2 Alignment and filtering
Genome indexing and mapping Align reads to a reference genome.
Filtering reads Remove duplicates, low-quality and blacklisted regions.
Library quality metrics Check enrichment and replicate agreement.
Signal tracks Create coverage files for genome-browser viewing.
Module 3 Peak calling
Control and input samples Why a control matters and how it is used.
Narrow and broad peaks Choose settings for transcription factors vs histone marks.
Replicates Combine replicates into a reliable peak set.
Reviewing peaks Inspect calls visually and tune thresholds.
Module 4 Annotation and motifs
Annotating peaks Link peaks to nearby genes and genomic features.
Motif discovery Detect the DNA patterns the protein recognises.
Functional enrichment Find pathways and processes behind bound genes.
Profile plots and heatmaps Show signal around peaks and gene starts.
Module 5 Differential binding
Count matrices Quantify signal across a shared set of regions.
Statistical testing Identify gained and lost binding sites.
Comparing marks and conditions Overlap peak sets and interpret the differences.
Integrating expression Connect binding changes to gene activity.
Module 6 Mini-project and report
Week 4
Project dataset Work through a complete analysis on public data.
Reproducible workflow Record steps and settings so the work can be repeated.
Figures and report Prepare publication-style figures and a short write-up.
Review and next steps Discuss results and how to extend the analysis.

What you receive & prerequisites

What you receive

  • 30 days of structured online self-paced access & mentor guidance
  • Curated real-world NGS benchmark datasets
  • Reusable pipeline scripts and command-line code templates
  • Independent capstone mini-project evaluation
  • Certificate of Completion issued by Xenoi Biotech Pvt. Ltd.

Prerequisites & setup

  • Basic life science background (B.Sc., M.Sc., B.Tech, or research scholar)
  • No prior programming or Linux experience required (covered in Module 1)
  • Laptop or PC with 8 GB RAM and internet access
  • Remote compute setup instructions provided during onboarding

Course curriculum designed by Anjali Chaudhary, Bioinformatics Scientist at Xenoi Biotech.

Last updated: October 2026

Related workshops & services

Broaden your computational biology expertise with complementary workshops:

Need this analysis done for your laboratory data? Explore our Genomics Services or consult on Custom Bioinformatics Pipelines.

Frequently asked questions

Is this ChIP-Seq workshop delivered online?

Yes. All Xenoi Biotech workshops are delivered 100% online, allowing researchers and students across India and internationally to participate with remote compute support.

How long is the workshop and what is the workload?

The workshop runs for 30 days across 6 structured modules. Learners typically dedicate 1 to 2 flexible hours per day to work through pipeline commands, code exercises, and the mini-project.

Who is this workshop designed for?

It is built for B.Sc., M.Sc., and Ph.D. students, postdoctoral researchers, faculty members, and industry professionals in biotechnology, biochemistry, microbiology, and medicine who need to analyze NGS datasets independently.

What will I learn in this workshop?

You will learn alignment with Bowtie2, PCR duplicate removal, broad and narrow peak calling with MACS3 against input controls, peak annotation in ChIPseeker, de novo motif discovery with MEME, and differential binding analysis in DiffBind.

What are the fees, dates, and enrollment details?

The workshop fee is MRP ₹5,000, inclusive of GST. Batch dates are shared on enquiry. Use the Enrol now button to reserve your place or receive the upcoming schedule.

Fees, dates and batches

The workshop fee is MRP ₹5,000 (incl. GST). Batch dates and onboarding materials are shared upon enquiry.

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