Introduction to RNA-seq using High-Performance Computing (HPC) · Learning objectives Learning...

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Introduction to RNA-seq using High-Performance Computing (HPC) Harvard Chan Bioinformatics Core in collaboration with HMS Research Computing https://tinyurl.com/intro-to-rnaseq-adv

Transcript of Introduction to RNA-seq using High-Performance Computing (HPC) · Learning objectives Learning...

Page 1: Introduction to RNA-seq using High-Performance Computing (HPC) · Learning objectives Learning Objectives Describe best practices for designing a bulk RNA-seq experiment Describe

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

Harvard Chan Bioinformatics Core in collaboration with

HMS Research Computing

https://tinyurl.com/intro-to-rnaseq-adv

https://tinyurl.com/intro-to-rnaseq-adv
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Rory KirchnerJohn HutchinsonAssociate Director Victor BarreraShannan Ho Sui

Director Zhu Zhuo

James Billingsley Peter KraftFaculty AdvisorSergey NaumenkoIlya Sytchev Joon Yoon

Radhika KhetaniTraining DirectorMary PiperMeeta Mistry Jihe LiuPreetida Bhetariya

Page 3: Introduction to RNA-seq using High-Performance Computing (HPC) · Learning objectives Learning Objectives Describe best practices for designing a bulk RNA-seq experiment Describe

Rory KirchnerJohn HutchinsonAssociate Director Victor BarreraShannan Ho Sui

Director Zhu Zhuo

James Billingsley Peter KraftFaculty AdvisorSergey NaumenkoIlya Sytchev Joon Yoon

Radhika KhetaniTraining DirectorMary PiperMeeta Mistry Jihe LiuPreetida Bhetariya

Page 4: Introduction to RNA-seq using High-Performance Computing (HPC) · Learning objectives Learning Objectives Describe best practices for designing a bulk RNA-seq experiment Describe

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

We have divided our short workshops into 2 categories:

1. Basic Data Skills - No prior programming knowledge needed (no prerequisites)

2. Advanced Topics: Analysis of high-throughput sequencing (NGS) data - Certain “Basic” workshops required as prerequisites.

Any participants wanting to take an advanced workshop will have to have taken the appropriate basic workshop(s) within the past 6 months.

https://hbctraining.github.io/main/training_spring2019.html http://bioinformatics.sph.harvard.edu/training/

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

https://hbctraining.github.io/main/training_spring2019.html#basic-data-skills
https://hbctraining.github.io/main/training_spring2019.html#advanced-topics-analysis-of-high-throughput-sequencing-ngs-data
https://hbctraining.github.io/main/training_spring2019.html#advanced-topics-analysis-of-high-throughput-sequencing-ngs-data
https://hbctraining.github.io/main/training_spring2019.html#advanced-topics-analysis-of-high-throughput-sequencing-ngs-data
https://hbctraining.github.io/main/training_spring2019.html#basic-data-skills
https://hbctraining.github.io/main/training_spring2019.html
http://bioinformatics.sph.harvard.edu/training/
https://hbctraining.github.io/main/
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Setting up to perform Bioinformatics analysis

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

Page 8: Introduction to RNA-seq using High-Performance Computing (HPC) · Learning objectives Learning Objectives Describe best practices for designing a bulk RNA-seq experiment Describe

Standards✓ Introduction to the command-line interface (shell, Unix, Linux)

• Dealing with large data files

• Performing bioinformatics analysis• Using 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

Setting up…

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Workshop scope

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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 a bulk RNA-seq experiment

✓ Describe steps in an RNA-seq analysis workflow (from sequence data to expression quantification).

✓ Implement shell scripts on a high-performance compute cluster to perform the above steps.

We won’t be covering how to perform differential gene expression (DGE) analysis on count data in this workshop. A DGE workshop will be held on October 21st/22nd and the pre-requisite for it is a working knowledge of R (October 3rd/4th).

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Logistics

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https://tinyurl.com/intro-to-rnaseq-adv

Course webpage (wiki)

https://tinyurl.com/intro-to-rnaseq-adv
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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 ✤ Phones on vibrate/silent!

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• Andy Bergman & Kathleen Keating from 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]

O2 (HMS-RC): [email protected]

HBC consulting: [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

Practical RNA-seq analysis

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Tutorial - QIAGEN Bioinformatics€¦ · Four workflows: 1.RNA-Seq and IPA analysis workflow 2.RNA-Seq and IPA advanced analysis workflow 3.RNA-Seq analysis workflow 4.RNA-Seq analysis

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Introductiontodifferentialgeneexpressionanalysisusing RNA-seq · Figure 1 RNA-seq work flow. (a) Schematic diagram of RNA-seq library construction. Total RNA is extracted from 300,000

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RNA- seq Analysis in Galaxy

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RNA-seq - Read mapping and · PDF fileRNA-seq (1) Peter N. Robinson Microarrays RNA-seq Alternative splicing mapping cu inks Bipartite RNA-seq Read mapping and Quanti cation Peter

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Differential analysis of RNA-Seq data: design, describe ...

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RNA-seq - Quantification and Differential · PDF fileRNA-seq (2) Peter N. Robinson RNA-seq RPKM Fisher’s exact test Poisson LRT Negative Binomial RNA-seq Quanti cation and Di erential

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Rna seq - PDX models

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Update - AH diagnostics...Advanta RNA-Seq NGS Library Prep on Juno RNA sequencing (RNA-seq) is the gold standard for hypothesis-free profiling of the transcriptome. Advanta™ RNA-Seq

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