EPIGENOMICS 30 days · 6 modules · Online

SNAP-ChIP Calibrated Data Analysis Workshop (30-Day, Online)

Quantify histone modifications with spike-in controls and compare conditions with calibrated chromatin signal.

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About this workshop

Standard ChIP-Seq is good at showing where a histone modification is, but it is poor at showing whether the total amount of that modification has changed between samples. Spike-in calibration solves this by adding a known set of reference nucleosomes, each carrying a defined modification, to every sample. Because the amounts are known, the reads they produce can be used to scale the data and to check how specific the antibody is. This workshop teaches how to count the spike-in reads, calculate scaling factors, build calibrated signal tracks and compare them with standard normalisation. You will see what calibration changes in practice, especially when a treatment alters a mark across the whole genome, and how to report such results with confidence.

Tools and pipelines you will use

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

Bowtie2 ↗Samtools ↗MACS3 ↗deepTools ↗DiffBind ↗

What you will learn

Module 1 Foundations
Week 1
Linux and command-line basics Run tools and manage files.
Histone modifications Common marks and what they indicate.
Spike-in principle How a known control makes samples comparable.
Read quality control Check and clean reads.
Module 2 Alignment and barcode counting
Genome mapping Align reads to the reference.
Spike-in sequence counting Count control reads for each sample.
Antibody specificity checks Judge off-target signal from the controls.
Filtering Remove duplicates and unreliable reads.
Module 3 Calibration and normalization
Calculating scaling factors Use control counts to rescale samples.
Applying calibration Generate calibrated signal tracks.
Comparing with standard normalization See what calibration changes.
Quality checks Confirm that replicates agree.
Module 4 Signal profiling
Peak and domain calling Find enriched regions for each mark.
Signal around genes Profile marks across gene bodies and starts.
Heatmaps and metaplots Visualize patterns across thousands of regions.
Annotation Link regions to genes and features.
Module 5 Comparative analysis
Global changes in a mark Detect genome-wide gain or loss.
Local differences Find regions that change between conditions.
Combining marks Relate activating and repressive marks.
Interpretation Connect changes to expression and function.
Module 6 Mini-project and report
Week 4
Project dataset Analyse a calibrated ChIP dataset.
Reproducible workflow Record every step and setting.
Figures and write-up Present calibrated results clearly.
Review and next steps Discuss controls and follow-up.

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 SNAP-ChIP 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 to quantify synthetic spike-in nucleosome barcodes, evaluate antibody specificity on-target vs off-target, compute linear scaling factors, generate calibrated bigWig coverage tracks in deepTools, and test differential global marks.

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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