School of Bioinformatics · Genomics & transcriptomics
Epigenomics: ChIP-seq, ATAC-seq & DNA Methylation
Epigenomic assays measure how DNA is packaged, bound and chemically marked. This course covers the analysis of protein–DNA binding, chromatin accessibility and DNA methylation, and how to connect them to gene regulation.
Course overview
Epigenomics teaches the shared logic of enrichment-based assays (ChIP-seq, CUT&RUN and ATAC-seq): alignment, fragment-size checks, peak calling against the right control, reproducibility between replicates and differential analysis.
The course then turns to bisulfite and enzymatic methylation sequencing, and closes with integration: linking peaks and methylation to nearby genes, finding enriched motifs and testing whether regulatory changes explain expression changes.
Learning outcomes
By the end of the course you will be able to:
- Process and quality-check ChIP-seq, CUT&RUN and ATAC-seq data
- Call peaks with appropriate controls and assess replicate concordance
- Perform differential binding and accessibility analysis
- Analyse bisulfite sequencing and find differentially methylated regions
- Annotate regulatory regions, run motif enrichment and integrate with RNA-seq
Skills you will practise
Eligibility and prerequisites
Who can apply
- Students and graduates of B.Sc., M.Sc., B.Tech., M.Tech., B.Pharm., M.Pharm., MBBS, BDS, B.V.Sc. or a PhD programme in the life sciences, biotechnology, bioinformatics, pharmacy, medicine, agriculture, chemistry, statistics or computer science
- Researchers, faculty and industry professionals moving into data-driven biology
- Final-year students may apply before their results are declared
Prerequisites
- NGS Data Analysis or equivalent
- Basic R
Best suited to
- Researchers studying gene regulation, development or cancer epigenetics
- Bioinformaticians supporting chromatin assays
- PhD students with ChIP-seq or ATAC-seq data
Module-wise syllabus
6 modules. Each pairs instructor-led sessions with a hands-on lab on public data.
Topics
- ChIP-seq, CUT&RUN and ATAC-seq
- Controls and spike-ins
- Design and depth
Topics
- Alignment and duplicate handling
- Fragment sizes and TSS enrichment
- Blacklisted regions
Topics
- MACS3 narrow and broad peaks
- FRiP and IDR
- Consensus peak sets
Topics
- DiffBind and DESeq2 on peaks
- HOMER and MEME-ChIP motif enrichment
- Footprinting concepts
Topics
- Bisulfite and EM-seq chemistry
- Bismark alignment and methylation calls
- DMRs with methylKit
Topics
- Linking peaks to genes
- Integrating with RNA-seq
- Reporting
Practical sessions and projects
Capstone project
Explain a regulatory change
Combine chromatin accessibility, binding or methylation data with expression data to build and defend a mechanistic hypothesis about gene regulation.
Assessed on the correctness of the analysis, the quality of the code and the reasoning in the write-up. A pass is required for the certificate.
- Chromatin assays
Match public experiments to the questions they can answer and flag designs without proper controls.
- Processing and QC
Process an ATAC-seq run, plot its fragment-size distribution and compute TSS enrichment.
- Peaks and reproducibility
Call transcription-factor peaks in replicates and build an IDR-filtered consensus set.
- Differential analysis and motifs
Find regions that gain accessibility after a treatment and identify the motifs enriched in them.
- DNA methylation
Call methylation from bisulfite reads and find differentially methylated regions between two conditions.
- Project: a regulatory story
Integrate chromatin and expression data to propose, with evidence, how a regulator controls its target genes.
Software, tools and datasets
Software and tools
All software is free and open source or free for academic use. Recommended computer: 8 GB RAM, 30 GB free disk, Linux, macOS or Windows with WSL2.
Datasets
- ENCODE ChIP-seq and ATAC-seq experiments: Processing, peaks and differential analysis.ENCODE portal (public)
- Public bisulfite sequencing studies: Methylation practicals.GEO / SRA
Core reading
- Zhang Y et al. (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biology 9:R137.
- Buenrostro JD et al. (2013). Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin. Nature Methods 10:1213–1218.
- Krueger F, Andrews SR (2011). Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27:1571–1572.
Duration, format and fees
- Next cohort
- Dates are sent with your admission offer
- Timetable
- Three evening or weekend sessions a week (IST), plus a lab clinic; intensive and weekend-only schedules on request
- Payment
- Secure online payment link with your admission offer (UPI, cards, net banking). Instalments on request for fees above ₹15,000.
- Refunds
- See the refund and cancellation policy.
Instructor
The instructor for each cohort is named in your admission offer and on this page when the cohort is announced. Vedicgen instructors are selected for hands-on research or industry experience in the subject they teach, and every course is reviewed by a second subject expert.
Questions about who teaches a cohort? [email protected]
Certificate
Learners who complete the course and pass its capstone receive a Vedicgen certificate of completion for Epigenomics: ChIP-seq, ATAC-seq & DNA Methylation, issued by Vivofold, stating the guided hours and skills assessed. Each certificate has a unique ID and QR code that anyone can check.
Apply for Epigenomics: ChIP-seq, ATAC-seq & DNA Methylation
Apply
Send the form below. It takes about five minutes.
Review
An adviser confirms your fit and format within two working days.
Offer
You receive dates, timetable and a secure payment link.
Onboard
Set-up guide, pre-reading and joining links.
Frequently asked questions
In the live cohort, modules are taught in instructor-led sessions with a weekly lab clinic where you work on real public data with help at hand; every session is recorded. The self-paced format uses the same lessons, labs and datasets with mentor review of your capstone. Both formats end with an assessed project reviewed for the code and the science.
A laptop with at least 8 GB of RAM and about 30 GB of free disk space, running Linux, macOS, or Windows with WSL2. Installation instructions are sent before the first session, and lab clinics help with any set-up problems.
Yes. Learners who complete the course and pass its assessment receive a Vedicgen certificate of completion, issued by Vivofold. Every certificate carries a unique ID and a QR code that anyone, including an employer or admissions office, can check on the certificate verification page.
Apply with the form on this page. Live and in-person cohorts run through the year; the dates, timetable and joining details of the next cohort are sent with your admission offer and listed on this page once announced. Self-paced enrolment opens as soon as your application is accepted.
Yes. No course runs longer than four weeks, and the length is customisable: choose the standard schedule, an intensive one- to two-week schedule, weekends only, or a custom timetable. Pick your preference on the application form; colleges and teams can book their own dates.
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