BIO HELP LEARNING COURSE

ChIP-Seq Data Analysis Training

Master ChIP-seq analysis: QC, alignment, enrichment metrics, MACS3 peak calling, peak annotation, motif discovery and differential binding.

Genomics

◉ Beginner to Intermediate◷ 15 Hours / Live▣ Yes — Certificate of Completion

Course Information

Everything you need to know before enrolling.

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Live online classes
Group & college batches
Certificate on completion

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▤ Overview ☷ Curriculum ♙ Instructor ☆ Reviews ▣ FAQs

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About This Course

ChIP-seq identifies where transcription factors and histone marks bind across the genome. This 15-day training walks you through a professional ChIP-seq analysis workflow using widely used open-source tools.

You perform quality control, align reads with Bowtie2, assess ChIP enrichment against input, call peaks with MACS3, annotate and filter peaks, discover binding motifs with HOMER, visualize signal with deepTools and IGV, and compare binding between conditions in a final project.

Who this course is for

Students and researchers in epigenetics and transcriptional regulation
Lab scientists running ChIP-seq experiments
Learners with basic command-line knowledge

◎

What You’ll Learn

✓Understand the principles and applications of ChIP-Seq

✓Understand transcription factor binding and histone modification profiling

✓Perform quality control of ChIP-Seq FASTQ data

✓Perform read preprocessing and genome alignment

✓Generate and evaluate alignment files

✓Perform peak calling from ChIP-Seq data

✓Compare ChIP and control/Input samples

✓Visualize peaks in a genome browser

✓Annotate genomic peaks to nearby genes

✓Interpret ChIP-Seq results for regulatory genomics

⌘

Tools & Technologies

FastQCBowtie2SamtoolsMACS3deepToolsIGVHOMER

Course Curriculum

What you will learn, day by day

15 days 15 hours of training 60 topics Certificate on completion

- Protein–DNA interactions and histone marks
- Chromatin immunoprecipitation step by step
- Input controls and replicates
- Applications in gene regulation research
- FASTQ format and read characteristics
- Downloading public ChIP-seq datasets
- Treatment vs. input samples
- First look at read quality
- Running FastQC and MultiQC
- Adapter and quality trimming
- Checking duplication and library complexity
- Comparing reports before and after trimming
- Downloading and indexing the reference genome
- Aligning reads with Bowtie2
- Understanding alignment rates
- Handling multi-mapped reads
- SAM/BAM format explained
- Sorting, indexing and filtering with Samtools
- Removing PCR duplicates
- Alignment statistics
- Fingerprint plots for enrichment strength
- Cross-correlation (NSC/RSC)
- Library complexity metrics
- ENCODE quality guidelines
- Narrow vs. broad peaks
- Running MACS3 with an input control
- Key parameters and thresholds
- Peak output files
- FRiP score
- Removing blacklist regions
- Replicate concordance (IDR concept)
- Building a high-confidence peak set
- Annotating peaks to promoters, introns and intergenic regions
- Nearest-gene assignment
- Genomic distribution plots
- Distance-to-TSS analysis
- Extracting peak summit sequences
- De novo and known motif discovery with HOMER
- Interpreting motif enrichment
- Validating the immunoprecipitated factor
- Creating normalized bigWig tracks
- Heatmaps and profile plots
- Comparing ChIP and input signal
- Multi-sample visualization
- Loading tracks and peaks
- Inspecting binding sites at target genes
- Comparing conditions
- Exporting figures
- Comparing binding between conditions
- Count matrices for consensus peaks
- Statistical testing of differential binding
- Visualizing gained and lost sites
- Gene ontology of bound genes
- Pathway enrichment
- Integration ideas with RNA-seq
- Building the biological interpretation
- End-to-end analysis on a real dataset
- From raw reads to annotated peaks and motifs
- Writing the results report
- Presentation and feedback

♙

Your Instructor

Bio Help Learning Educator

Educator | Mentor

Learn from experienced educators and practitioners through practical, career-focused bioinformatics training.

Frequently Asked Questions

9 answers about this course

What is ChIP-Seq?

ChIP-Seq is a sequencing-based technique used to investigate protein-DNA interactions and genomic regions associated with transcription factors or histone modifications.

Who can join this ChIP-Seq training?

The course is suitable for biotechnology, bioinformatics, life science, genetics, genomics and related students, researchers and professionals.

Do I need prior ChIP-Seq experience?

No. The course begins with fundamental concepts and progresses toward practical data analysis.

Will this course include hands-on analysis?

Yes. The training focuses on practical ChIP-Seq data analysis using sequencing datasets.

Which tools will I learn?

You will work with FastQC, Bowtie2, Samtools, MACS3, deepTools, IGV and HOMER.

Will I learn peak calling?

Yes. Peak identification and quality assessment using MACS3 are included in the curriculum.

Will I learn motif analysis?

Yes. The course introduces motif discovery and transcription-factor binding analysis.

Will I learn genome-browser visualization?

Yes. You will learn to inspect ChIP-Seq peaks and genomic regions using IGV.

Will I receive a certificate?

Yes, participants can receive a certificate upon successful completion of the training.

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