Analysis Guides/

Hands-on Tour of the Single Cell Analysis Journey, From Cloud to Loupe to Community-Developed Tools

Mar 20, 2023
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Note: 10x Genomics does not provide support for community-developed tools and makes no guarantees regarding their function or performance. Please contact tool developers with any questions. If you have feedback about Analysis Guides, please email [email protected].

In this workshop, you will be introduced to the single cell gene expression analysis journey. Analysis begins at experimental design. Together we will explore a set of neutrophil data starting with the 10x Cloud Analysis platform for raw data processing. From there, we will assess the data quality using the Cell Ranger web summary and then move into the Loupe Browser for our initial analysis. We will take what we have learned from the Loupe analysis into the community-developed tools space where we will further explore neutrophil cell development with an RNA velocity analysis. To wrap things up, each participant will have the opportunity to map out their own analysis journey moving forward by sitting down with members of the Applied Bioinformatics team from 10x Genomics and local onsite bioinformaticians.

Introduction to the workshop and housekeepingWe will introduce the materials in this workshop including the dataset we will be exploring.
The slides can be found here. The data we are using is from the tech note here.
10x Genomics Cloud Analysis: from FASTQs to Quantitative Biological Information with Cell RangerWe will use the 10X Genomics Cloud Analysis resource to run our experiment. Here you will learn how to create a project, upload FASTQ files, run an analysis, and download the results.
There is also an analysis guide that covers this material here.
Introduction to Single Cell RNA-seq Data AnalysisWe will discuss 10x single cell technology, cover common questions that can be answered with single cell RNA-seq data, and discuss an example single cell RNA-seq analysis workflow.
A pdf version of these slides can be found here.
Quality assessment: interpreting the Cell Ranger web summaryWe will use the web_summary.html file output from Cell Ranger to assess the quality of an example single cell gene expression data.
You can also read the analysis guide on this page. More information about web summary can be found in this Technical note.
Loupe analysis: Quality control and rapid data explorationWe will use the Loupe Browser software to identify the neutrophil population in the data. We use as input the cloupe file which is produced by the Cell Ranger software. Within Loupe Browser we will use annotation and reclustering features to better understand the cell populations in this PBMC dataset.
The tutorial is also available on this page.
Further analysis using community developed tools: RNA velocityWe will discuss third party tools for data analysis downstream from Cell Ranger and Loupe. We will introduce an RNA velocity analysis and demonstrate an available resource for interacting with a Python-based analysis (jupyter notebook) in a Google Colab computing environment.
The tutorial materials for this video are located here. A pdf of these slides can be found here. Interactive notebook can be found in the link below:
Wrap up and planning your individual journeyAdditional resources: 10x Support site; Analysis guides
  • Ann Arbor, Michigan (July 20, 2022)
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