Published March 11, 2023 | Version 2.0.0
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hbctraining/Intro-to-ChIPseq-flipped: Understanding Chromatin Biology - Lessons from HCBC (2nd release)

  • 1. Harvard T.H. Chan School of Public Health

Description

Second release of the ChIP-seq data analysis training materials from the Harvard Chan Bioinformatics Core (https://bioinformatics.sph.harvard.edu/training). The raw data was obtained from the SRA (https://www.ncbi.nlm.nih.gov/sra?term=SRP134733).

Learning Objectives

  • Understand the necessity for, and use of, the command line interface (bash) and HPC for analyzing high-throughput sequencing data.
  • Understand best practices for designing a ChIP-seq experiment and analysis the resulting data.

Description This workshop focuses on teaching computational skills to enable the effective use of an high-performance computing environment to implement a ChIP-seq data analysis workflow. In addition to running the workflow from FASTQ files to peak calls, the workshop covers best practice guidelines for ChIP-seq experimental design and data organization/management and data visualization for quality control. Comparison with ATAC-seq and CUT&RUN methods were included in 2022.

  • Introduction to ChIP-seq
  • QC using FASTQC
  • Alignment and filtering of reads (Bowtie2, Samtools)
  • Peak calling (MACS2)
  • Peak overlap (bedtools)
  • Peak visualization (using deepTools)

Files

Intro-to-ChIPseq-flipped-chromatin-biology.zip

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