EPIGENOMICS 30 days · 6 modules · Online

Methyl-Seq DNA Methylation Workshop (30-Day, Online)

Align bisulfite sequencing reads, call cytosine methylation levels and find differentially methylated regions (DMRs).

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About this workshop

DNA methylation is a chemical tag on cytosines that helps control gene activity and changes with age, disease and environment. Bisulfite sequencing reads it out by chemically converting unmethylated cytosines so they can be told apart from methylated ones, which means the reads need aligners and quality checks built for that conversion. This workshop teaches how to prepare a converted reference, align reads, check conversion rates and coverage, and extract a methylation value for every cytosine. You then compare groups to find individual sites and wider regions, called differentially methylated regions, that differ, annotate them against genes and CpG islands, and ask whether methylation tracks with expression. It suits anyone studying epigenetic regulation.

Tools and pipelines you will use

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

Trim Galore ↗Bismark ↗Bowtie2 ↗methylKit ↗DSS ↗DMRcate ↗IGV ↗

What you will learn

Module 1 Foundations
Week 1
Linux and command-line basics Run tools and manage files.
DNA methylation biology What it does and where it occurs.
Bisulfite sequencing principle How methylation becomes a readable signal.
Read quality control Clean reads, including adapters.
Module 2 Bisulfite alignment
Reference preparation Build a converted genome index.
Mapping reads Align bisulfite-converted reads.
Duplicate handling Remove duplicates correctly for this data type.
Mapping quality Check conversion rate and coverage.
Module 3 Methylation calling
Extracting methylation calls Get a value for each cytosine.
Sequence contexts Separate CpG, CHG and CHH sites.
Coverage filtering Keep sites with enough reads.
Summary statistics Describe global methylation levels.
Module 4 Differential methylation
Site-level testing Find individual sites that differ between groups.
Region-level testing Detect differentially methylated regions.
Handling replicates and covariates Account for sample differences.
Visualization Plot methylation tracks and region profiles.
Module 5 Annotation and interpretation
Annotating regions Link results to promoters, genes and CpG islands.
Functional enrichment Interpret affected genes.
Combining with expression Test whether methylation tracks with gene activity.
Presenting findings Clear tables and figures.
Module 6 Mini-project and report
Week 4
Project dataset Analyse a public methylation dataset.
Reproducible workflow Record every step and setting.
Figures and write-up Present key regions and genes.
Review and next steps Discuss validation and limits.

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 Methyl-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 bisulfite-converted genome indexing, three-letter alignment with Bismark, conversion efficiency assessment from non-CpG cytosines, methylation extraction, and statistically sound DMR identification with methylKit and DSS.

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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