Summer 2022 Next Generation Sequencing Workshops

Summer 2022 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".

Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows you to profile the whole transcriptome of a large number of individual cells. However, the analysis of the large volumes of data generated from these experiments requires specialized statistical and computational methods. These workshops, taught by experienced Bioinformatics faculty, cover both the theoretical and practical aspects of a wide range of the computational workflows involved in processing scRNA-seq 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.

A familiarity with Linux and the Bash Shell is vital for these workshops. Submitting, monitoring, and managing jobs on the HTC cluster largely involves command-line operations. We do not routinely teach beginning Linux classes. If you are new to Linux environments, we highly recommend that you work your way through one of the past recordings (Introduction to Linux for NGS, Spring or fall 2021 workshop).

Register for all workshops: Summer 2022 NGS workshops

10X single cell techniques   

Instructor: Deborah Hollingshead, Director, Genomics Research Core

Monday June 27
11:00am – 1:00pm

This workshop will illustrate the technological basis of 10x genomics single cell analysis. I will also introduce  several chemistries 10X has developed for applications beyond single cell RNA-Seq and the sequencing read architecture of each application.
 
Single-cell Analysis with Seurat  

Instructor: Dhivyaa Rajasundaram, Bioinformatics Core Lead, UPMC Children’s Hospital

Tuesday June 28
11:00am – 1:00pm

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.

Single-Cell Analysis with Bioconductor   

Instructor: Uma Chandran, Director, Genomics Analysis Core and Cancer Bioinformatics Service

Wednesday June 29
11:00am – 1:00pm

This workshop will teach how to perform scRNAseq analysis using Bioconductor. The training will include many aspects of analysis such as normalization, cell type annotation of clusters, and pseudo-bulk differential gene expression. Similarities and differences to the Seurat pipeline will be mentioned.

Advanced Single-Cell Analysis 

Instructor: Wei Chen, Professor, Department of Pediatrics

Thursday June 30
11:00am – 1:00pm

This advanced workshop will focus on the analysis of multi-omics data and its integration (e.g. CITE-seq, multiome, and DOGMA-seq). The hands-on training will include background introduction and a step-by-step R pipeline with real applications from immunology.
 
Deep learning for scRNASeq analysis

Instructor: Yufei Huang, Leader, AI Research, UPMC Hillman Cancer Center

Friday July 1
11:00am – 1:00pm

This workshop will review the deep learning algorithms (variational autoencoder, autoencoder, generative adversarial network and supervised DL models ) and their applicability in the single cell RNA-seq processing pipeline. The hands-on training will provide examples to run deep learning RNASeq algorithms.