Spring 2021 Next Generation Sequencing Workshops | crc.pitt.edu

High throughput sequencing has brought abundant sequence data along with a wealth of new “-omics” protocols. Our nine hands-on, 3-hour workshops give researchers the 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.

Prior to the start of workshop, attendees should have:

Attendees are required to have a CRC account. To apply for an account, https://crc.pitt.edu/apply. You can follow the steps in this documentation to check if you have a CRC account, if you can login to the HTC cluster, and if you can submit jobs. Install Pulse Secure on your laptop so that you can access the HTC cluster.

R for genomics

Thursday, Feb. 18
1:00pm - 4:00pm

This is not an R programming workshop. This workshop will provide hands-on experience with the R and Bioconductor environment on the HTC cluster. We will present useful concepts for computations using the HTC cluster, and introduce RStudio and shiny servers on Open OnDemand. Presented by Fangping Mu.

~~Closed. Register: https://crc.pitt.edu/NGS-Spring-2021-Workshops-Register~~

Introduction to Linux for NGS

Tuesday, Feb. 23
1:00pm - 4:00pm

This workshop will also briefly cover UNIX skills, scripting, and job submissions using the HTC cluster. Presented by Uma Chandran.

~~Closed. Register: https://crc.pitt.edu/NGS-Spring-2021-Workshops-Register~~

RNASeq data analysis

Thursday, Feb 25
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.

~~Closed. Register: https://crc.pitt.edu/NGS-Spring-2021-Workshops-Register~~

Differential Expression and Functional Analysis

Tuesday, March 2
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.

~~Closed. Register: https://crc.pitt.edu/NGS-Spring-2021-Workshops-Register~~

Next Generation Sequencing

Tuesday, March 9
1:00 pm - 3:00pm

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.

~~Closed. Register: https://crc.pitt.edu/NGS-Spring-2021-Workshops-Register~~

Introduction to NGS data analysis

Thursday, March 11
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 using the HTC cluster. Presented by Riyue Bao.

~~Closed. Register: https://crc.pitt.edu/NGS-Spring-2021-Workshops-Register~~

Chipseq data analysis

Tuesday, March 16
1:00pm - 4:00pm

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.

~~Closed. Register: https://crc.pitt.edu/NGS-Spring-2021-Workshops-Register~~

Single cell RNASeq

Tuesday, March 23
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.

This workshop will present an overview of cellranger pipelines to process raw reads into expression values. Presented by Dhivyaa Rajasundaram.

~~Closed. Register: https://crc.pitt.edu/NGS-Spring-2021-Workshops-Register~~

scRNASeq data analysis

Thursday, March 25
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.