Archived Course

This course concluded in October 2024. The website is preserved for educational reference. Please contact our educational office if you are interested in a re-run of this course.

ScRNAseq in the Cloud: Pipelines to Insights 2024

This two-and-a-half day workshop will focus on using cloud infrastructure to carry single-cell RNASeq data from raw sequence files through count matrices to initial clustering of cell types, with a focus on workflows that emphasize best practices in rigorous and reproducible analysis.

October 23-25, 2024
MDI Biological Laboratory

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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.

The Dataset

Kimmel JC, Penland L, Rubinstein ND, Hendrickson DG, Kelley DR, Rosenthal AZ. Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging. Genome Res. 2019 Dec;29(12):2088-2103. doi: 10.1101/gr.253880.119. Epub 2019 Nov 21. PMID: 31754020; PMCID: PMC6886498.

Paper

Data

Schedule

October 23

Time	Activity
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	Intro to Nextflow & Pipelines
02:00-03:00	scrnaseq Pipeline Overview
03:00-04:00	Cloud Infrastructure Overview
04:00-04:30	Experiment Overview
04:30-05:00	Launch scrnaseq workflow

October 24

Time	Activity
9:00-9:30	Welcome \| Coffee/Tea \| Review of day-1
9:30-10:00	Overview of day-2
10:00-11:00	Keynote lecture-II by Dr. Prayag Murawala
11:00-11:30	Pipeline Execution Review
11:30-12:00	Debugging methodology & tips
12:00-01:00	Lunch
01:00-01:30	MDIBL Campus Tour
01:30-02:30	ScRNAseq Output Review
02:30-04:30	scscape Pipeline Overview
4:30-05:00	Launch scscape workflow

October 25

Time	Activity
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
12:30-01:30	Lunch & End of Workshop

Tuition

Category	Cost
INBRE	USD $300
Other academic/non-profit	USD $450
Industry/for-profit	USD $650

Note

The tuition includes all meals and housing.