Analysis Guides/

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

Apr 9, 2024
Share via:

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.

  1. Plan to bring a laptop to the event to participate, if you are attending the workshop in-person.
  2. Sign up for a 10X Cloud Analysis account.
  3. Download this tiny FASTQ data set to the computer you will have with you at the workshop.
  4. Download and install the latest Loupe Browser to the computer you will have with you at the workshop.
  5. Download this .cloupe file, which will be used during the workshop.
  6. Download the cell marker file BloodCell.csv, which will be used to annotate cell types during the workshop.
  7. Fill out the pre-workshop survey.
TopicsMaterialsPre-recorded videos
1. 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.
2. 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.
3. 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.
4. 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 guide on this page. The web summary we are using is from step 2 above. You can also view the web summary from here.
5. Loupe analysis: Quality control and rapid data explorationWe will use the Loupe Browser software to identify the neutrophil population in the data. 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. The loupe file we are using is from step 2 above. You can also download the loupe from here.
6. Further analysis using community developed tools: RNA velocityWe will discuss community tools for downstream data analysis. 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 is located here. A pdf of the slides can be found here. Interactive notebook can be found in this link.
7. Wrap up and planning your individual journeyAdditional resources: 10x Support site; Analysis guides

If you are interested in attending this workshop in-person, please complete the survey: Interest in In-Person Single-Cell Data Analysis Workshop. This information will be used to inform planning of future in-person workshops.

Local resources from selected past workshops

Stay connected with latest technical workflow and software updatesSubscribe to newsletter