Next Generation Sequencing Fall 2020 Workshops | crc.pitt.edu

These hands-on workshops will teach you practical skills to analyze NGS data using the HTC cluster.

You must bring your own laptop. The workshop will use the HTC cluster. Follow the steps in this document to check if you have a CRC account, if you can login to the HTC cluster, and if you can submit jobs. Request a new CRC account if you do not have one. Install Pulse Secure on your laptop so that you can access the HTC cluster on WIRELESS-PittNet network.

Prerequisite: A familiarity with Linux and the Bash Shell is vital for these workshops. To test your Linux/Bash familiarity, take the NIH HPC quiz. If you score below 8/10, we highly recommend that you work your way through one or more of the Linux tutorials.

R for genomics
Tuesday Sep. 15, 1-4 pm

This workshop will provide hands-on experience with RStudio server on Open OnDemand. We will present useful concepts for computations using the HTC cluster, and introduce the R and Bioconductor environment on the HTC cluster. Presented by CRC consultant Fangping Mu.

Single cell RNASeq
Thursday Sep. 17 1:00pm – 4:00pm

This workshop will discuss considerations for experimental design, the end goals of single cell analysis and cost estimates prior to sequencing. Presented by Robert Lafyatis, Director, Single Cell Core, Professor, Department of Medicine.

This workshop will introduce Cell Ranger and Loupe Browser. Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis. Loupe Browser is a desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Presented by Rosha Poudyal, PhD, Science & Technology Advisor, 10x Genomics

Introduction to R and RStudio server
Monday, Sep. 21, 1-4 pm

This workshop will provide an entry level introduction of R programming. In the first half, we will go over the concept of working environment, graphic user interfaces, operators, data types, conditionals and loops, functions and plotting. In the second half, we will focus on several practical examples. No programming background is required. Presented by Silvia Liu, Assistant Professor, Department of Pathology.

Chipseq data analysis
Friday, Oct. 9, 1-4 pm

This workshop will provide both theoretical and practical introduction to ChIP-seq data analysis. In the first section, we will present the principle of ChIP sequencing, bioinformatics pipeline of peak calling, data visualization, method of motif discovery, and a brief introduction of CUT&RUN sequencing. In the second half of the workshop, we will hand on a real ChIP-seq dataset to practice the pipeline using the HTC cluster. Presented by Silvia Liu, Assistant Professor, Department of Pathology

Somatic Variant identification and interpretation in cancer
Tuesday, Oct. 13, 1-4 pm

This workshop will provide an overview and hands-on practice for whole exome sequencing (WES) somatic variant calling in tumor tissues. In Part I, we will review key analysis steps, quality evaluation metrics, and statistical algorithms with a focus on the GATK4-MuTect2 best practices. Presented by Riyue Sunny Bao, Ph.D., Co-Director of Cancer Bioinformatics and Research Associate Professor of Medicine.

Thursday, Oct. 15, 1-4 pm

This workshop will introduce tools, resources, and approaches to interpret somatic variants generated in Session I. In Part I, we will review publicly available cancer genomic databases and methods to integrate them with clinical data for the biological interpretation of the variants. In Part II, we will run variant annotation/interpretation workflow via Unix / Linux commands and RStudio on the HTC cluster. Presented by Riyue Sunny Bao, Ph.D., Co-Director of Cancer Bioinformatics and Research Associate Professor of Medicine.

scRNASeq data analysis
Tuesday, Oct. 20, 1:00pm – 4:00pm
This workshop will familiarize participants with the basics of scRNAseq technologies, presenting an overview of pipelines to process raw reads into expression values. Presented by Dhivyaa Rajasundaram, Ph.D., research assistant professor in Pediatrics and core lead, Bioinformatics Core, UPMC Children’s Hospital.

Thursday, Oct. 22, 1:00pm – 4:00pm

The hands-on training will include reading the count data in R, quality control, normalization, dimensionality reduction, cell clustering, and finding marker genes. A comparison of the different analysis pipelines using Seurat, Scran, and Scanpy will be covered. It also includes the integrative analysis of simulated vs control data using the anchoring framework in Seurat V3. Presented by Dhivyaa Rajasundaram, Ph.D., research assistant professor in Pediatrics and core lead, Bioinformatics Core, UPMC Children’s Hospital.

ATACSeq data analysis
Tuesday, Oct. 27, 1-4 pm

This workshop will present the ATACseq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) method. The focus of the workshop will be on running ATAC-seq pipelines, from raw fastq files, to quality control, alignment to reference genome, peak calling and differential analysis.
Presented by CRC consultant Fangping Mu.

RNASeq data analysis
Tuesday, Nov. 3. 1:00pm – 4:00pm
This workshop will discuss considerations for experimental design and the end goals of analysis prior to sequencing. Basics of sequencing and cost estimates will be discussed in the experimental design process. Presented by Amanda Poholek, Director, Health Sciences Sequencing Core at UPMC Children's Hospital of Pittsburgh, Assistant Professor, Department of Pediatrics.
This workshop will also briefly cover UNIX skills, scripting, and job submissions. Presented by Uma Chandran, Director, Genomics Analysis Core and Cancer Bioinformatics Service, and research associate professor, Department of Biomedical Informatics.

Thursday, Nov. 5, 1:00pm – 4:00pm

The focus of the workshop will be on running RNA seq pipelines, from raw fast files, to fastqc, alignment to reference genome and generating gene expression counts. Presented by Uma Chandran, Director, Genomics Analysis Core and Cancer Bioinformatics Service, and research associate professor, Department of Biomedical Informatics.

Differential Expression Analysis
Tuesday, Nov. 10, 1-4 pm

This hands-on workshop will introduce participants to statistical methods and considerations used to perform differential gene expression analysis on bulk RNA-seq data using edgeR, and DESEQ2. The workshop will also provide an overview of tools for functional analysis of DE genes to make biological inferences from large gene lists. Presented by Dhivyaa Rajasundaram, Ph.D., research assistant professor in Pediatrics and core lead, Bioinformatics Core, UPMC Children’s Hospital.