e-learning
Generating a single cell matrix using Alevin and combining datasets (bash + R)
Abstract
Setting up the environment
About This Material
This is a Hands-on Tutorial from the GTN which is usable either for individual self-study, or as a teaching material in a classroom.
Questions this will address
- I have some single cell FASTQ files I want to analyse. Where do I start?
- How to generate a single cell matrix using command line?
Learning Objectives
- Generate a cellxgene matrix for droplet-based single cell sequencing data
- Interpret quality control (QC) plots to make informed decisions on cell thresholds
- Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata
Licence: Creative Commons Attribution 4.0 International
Keywords: 10x, MIGHTS, Single Cell, jupyter-notebook, paper-replication
Target audience: Students
Resource type: e-learning
Version: 4
Status: Active
Prerequisites:
- Generating a single cell matrix using Alevin
- Introduction to Galaxy Analyses
Learning objectives:
- Generate a cellxgene matrix for droplet-based single cell sequencing data
- Interpret quality control (QC) plots to make informed decisions on cell thresholds
- Find relevant information in GTF files for the particulars of their study, and include this in data matrix metadata
Date modified: 2024-10-28
Date published: 2023-12-08
Contributors: Mehmet Tekman, Pavankumar Videm
External resources:
Activity log
