Epigenomics: ATAC-Seq & Methylation — Hands-on

Gain expertise in epigenomics using ATAC-Seq and DNA methylation workflows, from QC and peak calling to footprinting, DMR analysis, and reproducible reporting.

Epigenomics (ATAC-Seq, Methylation)

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Session Index

Session 1 — Library QC & Read Processing Session 2 — ATAC-Seq Peaks & Footprinting Session 3 — Bisulfite Mapping & DMRs Session 4 — Mini Capstone: Epigenomics Pipeline

Session 1

Fee: Rs 6300

Library QC & Read Processing

Experimental design, controls and metadata capture

Theory

FASTQ QC, trimming and adapter removal

FastQC MultiQC Cutadapt fastp

Alignment and duplicate handling for chromatin assays

Bowtie2 BWA-MEM2 Picard samtools

Session 2

Fee: Rs 8400

ATAC-Seq Peaks & Footprinting

Peak calling, TSS enrichment and FRiP metrics

MACS2 deepTools ATACseqQC

Motif analysis and transcription factor footprints

HOMER HINT-ATAC TOBIAS

Peak annotation and regulatory context

ChIPseeker GREAT bedtools

Session 3

Fee: Rs 11200

Bisulfite Mapping & DMRs

WGBS and RRBS library concepts and QC checks

Theory

Bisulfite aware alignment and methylation extraction

Bismark BS-Seeker2 Methyldackel

Differential methylation regions and annotation

methylKit DSS annotatr

Session 4

Fee: Rs 14000

Mini Capstone: Epigenomics Pipeline

Design an end to end ATAC and methylation workflow with provenance

Theory

Automate QC to peaks or DMRs with unified reports

Snakemake Conda/Mamba MultiQC

Publish ready figures and tables for regulatory interpretation

pandas ggplot2 R Markdown/Quarto

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Epigenomics (ATAC-Seq, Methylation) Training | Peaks, Footprints, Bisulfite Mapping & DMRs

Epigenomics: ATAC-Seq & Methylation — Hands-on