EPIGENOMICS 30 days · 6 modules · Online

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

Profile open chromatin, regulatory elements and the transcription factor networks that shape cell identity.

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About this workshop

ATAC-Seq maps open chromatin, the parts of the genome that are physically accessible to regulatory proteins, using a small amount of cells and a short protocol. Accessible regions often mark active promoters and enhancers, so the data reveals which parts of the genome a cell type is using. This workshop covers the analysis from raw reads to interpretation: quality checks that use fragment-size patterns, alignment and filtering, peak calling and building a reliable set of accessible regions. You then annotate peaks, search for enriched transcription factor motifs, examine footprints that hint at bound factors, and test for regions that open or close between conditions. Finally you learn to link accessibility to nearby genes and compare it with expression.

Tools and pipelines you will use

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

FastQC ↗Bowtie2 ↗Picard ↗MACS3 ↗deepTools ↗HOMER ↗TOBIAS ↗DiffBind ↗ChIPseeker ↗

What you will learn

Module 1 Foundations
Week 1
Linux and command-line basics Navigate files and run tools.
Chromatin accessibility What open chromatin tells you.
File formats FASTQ, BAM, BED and bigWig.
Read quality control Clean reads and check fragment sizes.
Module 2 Alignment and filtering
Mapping reads Align to the reference genome.
Filtering Remove mitochondrial reads, duplicates and low-quality reads.
Fragment size patterns Read nucleosome signals in your data.
Quality metrics Judge enrichment at gene starts.
Module 3 Peak calling
Calling accessible regions Detect open chromatin peaks.
Replicates Build a consistent peak set.
Signal tracks Create files for genome browsers.
Reviewing peaks Check calls against known regulatory regions.
Module 4 Annotation and motifs
Annotating peaks Place peaks in promoters, enhancers and other features.
Motif enrichment Find transcription factor motifs in open regions.
Footprinting Infer factor binding within accessible sites.
Functional enrichment Interpret nearby genes.
Module 5 Differential accessibility
Count matrices Quantify accessibility across regions.
Statistical testing Find regions that open or close between conditions.
Linking peaks to genes Connect accessibility to expression.
Visualization Heatmaps and example region plots.
Module 6 Mini-project and report
Week 4
Project dataset Analyse a public ATAC-Seq dataset.
Reproducible workflow Record every step and setting.
Figures and write-up Present accessibility changes and regulators.
Review and next steps Discuss validation and extensions.

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 ATAC-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 master the full open chromatin analysis pipeline from raw FASTQ quality control, Bowtie2 alignment, and mitochondrial read filtering to MACS3 peak calling, transcription factor motif discovery, digital footprinting with TOBIAS, and differential accessibility testing using 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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