Epigenetics in Galaxy

Shaurya Jauhari, PhD
August 22th 2020

Epigenetics ... Really !

Phenotype
- a physiological state (normal, diseased, treated)

Where are we coming from?

Ecker et al. 2012 (https://doi.org/10.1038/489052a)

Chromatin Immunoprecipitation (ChIP) Sequencing

Szalkowski and Schmid 2010 (https://doi.org/10.1093/bib/bbq068)

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ChIP-Seq Data Analysis

Kidder et al. 2011 (https://doi.org/10.1038/ni.2117)

DNA Methylation Data Analysis

ATAC-Seq Data Analysis

Open Chromatin
- DNase-Seq, FAIRE-Seq

Exercises

Installing tools in Galaxy: https://shauryajauhari.github.io/installing_tools_in_galaxy/
Quality Control: https://shauryajauhari.github.io/quality_control/
Mapping Data in Genomics: https://shauryajauhari.github.io/data_mapping/
DNA Methylation Data Analysis: https://shauryajauhari.github.io/dna_methylation_data_analysis/
ATAC-Seq Data Analysis: https://shauryajauhari.github.io/atac_seq_data_analysis/

Thank You

Data
This presentation can be reached at https://rpubs.com/shauryajauhari/epigeneticsGalaxy
Blog: https://shauryajauhari.github.io
Email: shauryajauhari@gzhmu.edu.cn