Fall 2021 Next Generation Sequencing Workshops

These workshops were supported in part by the University of Pittsburgh seed project titled "University of Pittsburgh Computational Genomics Training Program".

High throughput sequencing has brought abundant sequence data along with a wealth of new “-omics” protocols, and this explosion of data can be as bewildering as it is exciting. Our multi-day hands-on workshops give researchers the research, open-sourced tools to plan and execute successful bioinformatics and genomics experiments. These workshops, taught by experienced Bioinformatics core faculty, cover both the theoretical and practical aspects of a wide range of NGS data, using the HTC cluster.

These workshop have hands-on components that require the following requirements be set up before a workshop begins.

1. Participants should have an account on the HTC cluster, which is the cluster we will use for demonstration purposes. (page 1 of this documentation)
2. This workshop also requires that participants either be on a Pitt network (hard-line) or behind a VPN. (page 2 of this documentation)
3. You can submit jobs, i.e., your group’s account has not expired, and your group’s service units (CPU-hours) have not been exhausted entirely (page 4 of this documentation)

As a general rule, we offer no troubleshooting for technical setup issues at the workshops themselves! Therefore, be aware that if you do not set up the workshop's technical prerequisites well in advance, you may not be able to participate fully in its hands-on activities.

You can find the titles of past NGS workshops and links to their recordings. For each workshop, there may also be slides used in the workshop and other additional relevant resources.

Next Generation Sequencing and Single Cell Techniques

Tuesday, Sep. 14
1:00 pm - 4:00pm

This workshop will cover the basis of Next-Gen Sequencing Library Preparation for Illumina Sequencers. Different Library Preparation Techniques (DNA-seq, ChIP-seq, RNA-seq, Methyl-seq) are explained. Quality Control steps of the starting input material and final libraries are also explained. This workshop will also 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. 1:00pm - 2:30pm

This workshop will overview 10X genomics techniques for single cell sequencing, including RNA, ATAC, TCR, etc. The workshop will also highlight tips and potential approaches related to single-cell sequencing and introduce the major methods and tools available for single-cell sequencing. We will discuss considerations for experimental design, the end goals of single cell analysis and cost estimates using the single-cell applications on the NovaSeq and the NextSeq 500 sequencers. Presented by Robert Lafyatis. 2:30pm – 4:00pm

Overview of NGS data analysis using Pitt ondemand and python

Thursday, Sep. 16
1:00 pm - 4:00pm
This workshop will provide general workflows of NGS data analysis using Pitt ondemand and the HTC cluster. I will briefly introduce ondemand file management, various genomics apps and Jupyter notebooks/lab. A hands-on session to run scanpy through Jupyter notebook will follow. We will then go through the command line interface of the HTC cluster, focusing on python programming and conda package management. We will conclude the workshop with a second hands-on session to run Jupyter Lab through ondemand. Presented by Fangping Mu.

Introduction to Linux for NGS

Tuesday, Sep. 21
1:00pm - 4:00pm

This workshop introduces the basic concepts of Linux operating system and shell scripting. We will explore essential hands-on skills to confidently use the command line interface on a remote HTC cluster running the Linux system. Next, this workshop covers how to navigate around the Unix file system from the command line and use a number of basic, common Unix commands. This workshop will briefly cover job submissions to the HTC cluster. The course is supplemented with many hands-on examples. Presented by Uma Chandran.

RNASeq data analysis

Tuesday, Sep. 28
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. To facilitate learning, the workshop will be centered on hands-on tutorial that will guide students in processing the data from raw reads through read counts using a real case study based approach appropriate for Illumina read data. Presented by Uma Chandran.

Differential Expression and Functional Analysis

Tuesday, Oct. 5
1:00pm - 4:00pm

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 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.

Introduction to NGS data analysis

Thursday, Oct. 14
1:00pm - 4:00pm

High-throughput sequencing technology involves a number of concepts and techniques that shape a project before application-specific processes are utilized. This workshop covers common file formats for sequence data and limitations of sequencing technologies. This workshop introduces the more “universal” aspects of high-throughput sequence analysis. We will explore a hands-on exercise focusing on DNAseq data processing. Presented by Riyue Bao.

ChIP-seq and ATAC-seq data analysis

Tuesday, Oct. 26
1:00pm - 4:00pm

This workshop will provide both theoretical and practical introduction to ChIP-seq and ATAC-Seq data analysis. In the first section, we will present the principle of ChIP and ATAC 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.

scRNASeq data analysis using R 

Tuesday, Nov. 2
1:00pm - 4:00pm

This workshop will briefly review the cellranger pipelines to process raw reads into expression values. The hands-on training will include reading the count data in R, quality control, normalization, dimensionality reduction, cell clustering, and finding marker genes. The Seurat pipeline 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.