Bioinformatics Workshop: Basics of 10X scRNA-Seq Analysis

Genomics/Bioinformatics Seminar being offered in September 2024

Sept 27, 2024 - So you want to do a: PacBio RNAseq Experiment

 

Basic Information:

August 28 - 30, Wednesday, Thursday, 9 am to 3 pm, and Friday, 9 am to Noon.

Organizer - UCSF CAT Bioinformatics

Contact - [email protected]

Location - Genentech Hall, Teaching Lab Room 227

Cost - By application, $800 (UC Rate), Other Academic/Non-Profit ($1000), For-Profit ($1500) per person

   via CAT iLabs submission (after acceptance), a Credit Card option is not available this time.

Seats Available - 25 Seats

Registration: Basics of Bulk RNA-Seq Analysis

Workshop Description:

This 2.5-day in-person workshop includes a half-day of introductory material, followed by two days of focused, in-depth coursework on 10x single-cell RNA-seq. Participants will explore experimental design, data generation, data reduction, and basic analysis of single-cell RNA sequencing data using the command line and the R statistical programming environment. The course will cover software and protocols, workflow creation and modification, and diagnosing/treating problematic data using the command line and R code using Seurat. A basic understanding of the command line and R is highly recommended for success in this course. We will conduct a very brief review on the first morning, but we will not be providing full instruction in basic CLI or R.

Structure:

  • Day 1 (Morning): Introductory Material
  • Day 1 (Afternoon): Data reduction using 10X CellRanger and basic QA/QC
  • Day 2 to Day 3 (Morning): In-depth R Coursework on scRNA-seq with Suerat.

Sprinkled within will be talks and conversations, including experimental design, technology usage, and philosophy of analysis.

Focus Areas:

  • Experimental Design
  • Data Generation and Processing
  • Data Analysis using the R package Seurat.

Learning Objectives:

  • Conduct scRNA-Seq experiments using the command line and R.
  • Create and modify Illumina 10X sequencing data processing workflows.
  • Diagnose and address problematic data.

Prerequisites

  • Recommended: Basic understanding of the command line (CLI) and R.
  • Intermediate Knowledge: Needed for maximum value from the course.
  • Beginners: Can achieve a thorough understanding but may not be able to independently conduct an experiment.

Supplies Needed

  • A laptop with the command line terminal and R/Rstudio preinstalled.
  • We will have a dataset to use for the course, however you can bring your dataset for discussion purposes and feedback.

Recommendations for Beginners

  • Enroll in introductory courses in CLI and/or R courses to get the maximum out of the course.

 

Cancellation Policy:

Registrants are requested to be cognizant that only so many seats for a workshop may be available and should notify the Core ([email protected]) as soon as they know they are unable to attend so that we can notify and accept someone on the waitlist that a spot has become available.

Referencing the CAT Core and Publications

When submitting manuscripts, please acknowledge the CAT by including the text: “Sequencing was performed at the UCSF CAT, supported by UCSF PBBR, RRP IMIA, and NIH 1S10OD028511-01 grants.” 

 

To aid our facility in future grant submissions, it helps to reference labs and publications that have benefited from our core please notify us of your achievement by emailing catcore [at] ucsf.edu the PMID number, lab, and the piece of equipment used in the paper.