e-learning
Generating a single cell matrix using Alevin
Abstract
This tutorial will take you from raw FASTQ files to a cell x gene data matrix in AnnData format. What's a data matrix, and what's AnnData format? Well you'll find out! Importantly, this is the first step in processing single cell data in order to start analysing it.
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?
Learning Objectives
- Generate a cell by gene matrix for droplet-based single-cell RNA sequencing data
- Interpret quality control (QC) plots to make informed decisions on cell thresholds
- Find relevant information in GTF files for the experiment, and add this information into the metadata of the data matrix
Licence: Creative Commons Attribution 4.0 International
Keywords: MIGHTS, Single Cell, paper-replication
Target audience: Students
Resource type: e-learning
Version: 24
Status: Active
Prerequisites:
- An introduction to scRNA-seq data analysis
- Introduction to Galaxy Analyses
- Understanding Barcodes
Learning objectives:
- Generate a cell by gene matrix for droplet-based single-cell RNA sequencing data
- Interpret quality control (QC) plots to make informed decisions on cell thresholds
- Find relevant information in GTF files for the experiment, and add this information into the metadata of the data matrix
Date modified: 2025-05-07
Date published: 2021-03-03
Contributors: Beatriz Serrano-Solano, Björn Grüning, David López, Helena Rasche, Jonathan Manning, Julia Jakiela, Marisa Loach, Mehmet Tekman, Pavankumar Videm, Saskia Hiltemann, Teresa Müller, Wendi Bacon
Scientific topics: Transcriptomics
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