Introduction to ChIP-seq using High-Performance Computing ... · Describe best practices for...

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Introduction to ChIP-seq using High-Performance Computing (HPC) Harvard Chan Bioinformatics Core in collaboration with HMS Research Computing https://tinyurl.com/hbc-chipseq-schedule

Transcript of Introduction to ChIP-seq using High-Performance Computing ... · Describe best practices for...

Page 1: Introduction to ChIP-seq using High-Performance Computing ... · Describe best practices for designing an ChIP-seq experiment Describe steps in a typical ChIP-seq analysis workflow

Introduction to ChIP-seq using High-Performance Computing (HPC)

Harvard Chan Bioinformatics Core in collaboration with

HMS Research Computing

https://tinyurl.com/hbc-chipseq-schedule

https://tinyurl.com/hbc-chipseq-schedule
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Mary Piper

John Hutchinson Brad Chapman

Peter KraftRory Kirchner

Meeta Mistry Radhika Khetani

Shannan Ho Sui

Victor Barrera

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Consulting

• RNA-seq, small RNA-seq and ChIP-seq analysis

• Genome-wide methylation

• WGS, resequencing, exome-seq and CNV studies

• Quality assurance and analysis of gene expression arrays

• Functional enrichment analysis

• Grant support

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NIEHS / CFAR Bioinformatics

Core

Center for Stem Cell

Bioinformatics

Harvard Catalyst

Bioinformatics Consulting

HMS Tools &

Technology

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Training

• Short workshops on introductory, intermediate and

advanced topics related to NGS data analysis

• Monthly, 2-3 hour, hands-on and free workshops

on “Current Topics in Bioinformatics”

• In-depth courses (8- or 12-day formats)

http://bioinformatics.sph.harvard.edu/training/

https://hbctraining.github.io/main/

http://bioinformatics.sph.harvard.edu/training/
https://hbctraining.github.io/main/
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NIEHS / CFAR Bioinformatics

Core

Center for Stem Cell

Bioinformatics

Harvard Catalyst

Bioinformatics Consulting

HMS Tools &

Technology

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Workshop scope

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Setting up to perform Bioinformatics analysis

http://anoved.net/tag/lego/page/3/

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Standards✓ Introduction to the UNIX shell

• Dealing with large data files

• Using bioinformatics tools

• Accessing and using compute clusters

✓ R• Parsing and working with smaller results text files

• Statistical analysis, e.g. differential expression analysis

• Generating figures from complex data

Base components

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Bioinformatics data analysis

http://anoved.net/tag/lego/page/3/

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Learning objectives

Learning Objectives

✓ Describe best practices for designing an ChIP-seq experiment

✓ Describe steps in a typical ChIP-seq analysis workflow

✓ Use HMS-RC’s O2 compute cluster to efficiently run the ChIP-seq workflow from sequence reads to peak calls, including QC and visualization.

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Logistics

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https://tinyurl.com/hbc-chipseq-schedule

Course schedule

https://tinyurl.com/hbc-chipseq-schedule
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Course materials online

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The 2 Window problem…

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Odds and Ends

✤ Name tags: Tent Cards ✤ Post-its ✤ Wi-Fi: HMS Public ✤ Lunch locations ✤ Bathrooms ✤ Water Fountain ✤ Phones on vibrate/silent!

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• Shannan Ho Sui (HBC)• Andy Bergman (HMS-RC) • Kathleen Keating (HMS-RC) • Data Carpentry

Thanks!

These materials have been developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC). These are open access materials distributed under the terms of the Creative Commons Attribution license (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

http://www.datacarpentry.org/
http://bioinformatics.sph.harvard.edu/
http://bioinformatics.sph.harvard.edu/
http://creativecommons.org/licenses/by/4.0/
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Contact us!

HBC training team: [email protected]

HBC consulting: [email protected]

O2 (HMS-RC): [email protected]

HBC: @bioinfocore HMS-RC: @hms_rc

Twitter

mailto:[email protected]?subject=
mailto:[email protected]?subject=
mailto:[email protected]?subject=
https://twitter.com/bioinfocore
https://twitter.com/hms_rc

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