Analysis of single cell ATAC-seq data
03/06/2024
04/06/2024
General context
This course is an introduction to single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) data. The advantage over bulk ATAC-seq is that scATAC-seq gives cell-type-specific information, but it requires specific tools to analyze this data. ScATAC-seq can be integrated with scRNA-seq to retrieve gene regulatory information.
This course will guide you through the bioinformatics analysis of scATAC-seq data in R, using ArchR. We will also take you through the results obtained by CellRanger-ATAC. This course will make you acquainted with scATAC-seq data and will help you apply it to your own data in the end.
Participants should have basic experience with
- R: contact Janick.Mathys@vib.be if you want to follow the R introduction training
- NGS data analysis: contact Janick.Mathys@vib.be if you want to follow the NGS introduction training
- HPC on the VSC: contact Janick.Mathys@vib.be if you have never worked on the Vlaamse Super Computer
If the participant wishes to integrate scRNA-seq data with scATAC-seq data, they should have experience with single cell RNA-seq data analysis. Contact Janick.Mathys@vib.be if you want to follow the ‘analysis of single cell RNAseq data’ course.
Trainers
Hanne Puype
Hanne Puype is doing a PhD in Bioinformatics in the Lab for Computational Biology, Integromics and Gene Regulation (CBIGR) at UGent and has a background in biomedical sciences. She is passionate about the intersection between bioinformatics and human biology and has expertise in analyzing bulk and single-cell next-generation sequencing data.
Vanessa Vermeirssen
Vanessa Vermeirssen is professor at Ghent University. Her lab focusses on computational and high-throughput biological methods for single cell, multi-omics analysis with a focus on understanding gene regulation and signaling towards personalized medicine.
Program
Theoretical intro technology scATAC-seq
Theoretical intro data analysis scATAC-seq in R
Arrow files and quality control
Doublet inference
Dimensionality reduction, clustering and visualization
Cell type annotation using gene scores
Visualizing Genome Browser tracks
Calling peaks
Identifying marker peaks
Theoretical intro regulatory programs from scATAC-seq and scRNA-seq
Motif enrichment
Peak co-accessibility
Integration with scRNA-seq and peak-to-gene links
Work on own data
Practical info
03 June 2024 - 04 June 2024
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
03 June 2024 - 04 June 2024
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
03 June 2024 - 04 June 2024
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
03 June 2024 - 04 June 2024
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.
03 June 2024 - 04 June 2024
Ghent - VIB/UGent FSVM II
Room L4 of the FSVM2 building, Technologiepark, Gent