ScRNAseq in the Cloud: Pipelines to Insights 2024

Overview

Join us for a comprehensive workshop on utilizing cloud computing resources to analyze single-cell RNA sequencing (ScRNAseq). This workshop will primarily focus on the compute-intensive aspects of the analysis, including quality control (QC) and generating count matrices. These crucial workflow steps are often overlooked in single-cell omics courses. Participants will learn to leverage cloud infrastructure to ensure rigorous and reproducible results, from processing raw sequencing data to creating high-quality count matrices and performing initial clustering.

Additionally, the workshop will present a new Nextflow ScRNAseq clustering pipeline, designed to automate and efficiently carry out downstream analysis, including filtering, clustering, and preliminary cell type identification. After attending, you will have the skills and confidence to rigorously and reproducibly manage and analyze ScRNAseq data with precision, using the power of cloud computing to enhance your research.

Course Director

Course Faculty

Tentative Schedule

October 23

9:00-9:30   – Welcome | Coffee/Tea | Orientation
9:30-10:00  – Agenda/Course logistics
10:00-11:00 – Introduction to Single-cell omics
11:00-12:00 – Keynote lecture-I by Dr. Iain Drummond
12:00-01:00 – Lunch
01:00-02:00 – scrnaseq workflow overview (nextflow & pipeline concepts)
02:00-04:00 – Cloud infrastructure setup
04:00-04:30 – Experimental setup overview
04:30-05:00 – Launch scrnaseq workflow

October 24

9:00-9:30   – Welcome | Coffee/Tea | Review of day-1
9:30-10:00  – Overview of day-2
10:00-10:30 – Pipeline review (resiliency, cost analysis, failed jobs analysis if any)
10:30-11:00 – Debugging methodology & tips
11:00-12:00 – scrnaseq output QC review (multiqc, count matrices)
12:00-01:00 – Lunch
01:00-01:30 – MDI campus tour
01:30-02:30 – Keynote lecture-II by Dr. Prayag Murawala
02:30-04:30 – Downstream normalization & statistics (seurat)
4:30-05:00 – Launch scscape workflow

October 25

9:00-9:30   – Welcome | Coffee/Tea | Review of day-2
9:30-10:00  – Overview of day-3
10:00-10:30 – Loupe browser introduction
10:30-12:30 – Loupe browser exploration (validation logs, QC plots, PCA)
12:30-01:30 – Lunch & End of workshop

Tuition

INBRE: USD $300

Other academic/non-profit: USD $450

Industry/for-profit: USD $650

The tuition includes all meals and housing.

Partners