TRANSCRIPTOMICS 30 days · 6 modules · Online

PSI-Seq Splicing Data Analysis Workshop (30-Day, Online)

Detect alternative splicing events, calculate percent spliced in (PSI) and test differential splicing across conditions.

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About this workshop

One gene can produce several different transcripts when its exons are joined in different ways. This alternative splicing helps explain how a limited set of genes gives rise to so much biological variety, and splicing changes are linked to many diseases. In this workshop you learn to detect splicing events from RNA-Seq reads, from mapping across exon junctions to building a catalogue of events such as skipped exons and retained introns. You then calculate percent spliced in, the measure of how often an exon is included, and test whether it changes between conditions. You also learn how to judge when coverage is too low to trust a value, how to visualise splicing, and how to relate a change to the protein domains it affects.

Tools and pipelines you will use

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

STAR ↗rMATS ↗Whippet ↗SUPPA2 ↗DEXSeq ↗rmats2sashimiplot ↗

What you will learn

Module 1 Foundations
Week 1
Linux and command-line basics Run tools and manage files.
Splicing biology Exons, introns and how alternative splicing works.
Event types Skipped exons, retained introns and others.
Read quality control Clean reads before analysis.
Module 2 Splice-aware alignment
Aligning across junctions Map reads that span exons.
Junction discovery Find known and novel splice junctions.
Alignment quality Check junction coverage and depth.
Visual inspection View splice patterns in a browser.
Module 3 Event detection
Building an event catalogue List all possible splicing events.
Isoform expression Estimate transcript-level abundance.
Filtering low-support events Reduce false calls.
Combining replicates Merge evidence across samples.
Module 4 Percent spliced in
What PSI means Understand the inclusion measure.
Calculating PSI Compute inclusion levels per event.
Reliability and coverage Judge when a PSI value can be trusted.
Summary tables Organise events per gene and sample.
Module 5 Differential splicing
Statistical comparison Test changes in inclusion between groups.
Thresholds Combine significance and effect size.
Visualization Sashimi-style plots and event plots.
Functional impact Link splicing changes to domains and pathways.
Module 6 Mini-project and report
Week 4
Project dataset Analyse splicing in a public dataset.
Reproducible workflow Keep settings and versions together.
Figures and write-up Present top events and impact.
Review and next steps Plan validation, for example by PCR.

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 PSI-Seq (alternative splicing) 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 exon junction alignment in STAR, splice event classification (skipped exon, mutually exclusive exons, retained introns), PSI estimation and differential testing in rMATS and SUPPA2, and sashimi plot generation for publication figures.

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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