Educators:
Pavankumar Videm, Cristobal Gallardo Alba, Mehmet Tekman (RBC), Anne Fiebig (GCBN), Anton Nekrutenko, Fotis Psomopoulos, Florian Heyl, Peter van Heusden, Amazon Polly, Wendi Bacon
Date:
April 19-23, 2021
Location:
Online Training
Content:
It will be a one-week event introducing (sc)RNA-Seq concepts and demonstrate detailed data analysis using Galaxy. The sessions will be recorded with live support in chat, in which experts will answer questions on a peer-to-peer basis. The workshops will make use of the European Galaxy server and the Galaxy Training Material. Both will stay accessible and open after the training.
- Introduction to the Galaxy data analysis platform
- Crash course in sequencing technologies from a data analysts view
- Preprocessing of raw sequencing reads: quality control, adapter clipping, quality trimming
- Introduction to read mapping and visualization of mapped reads
- Introduction to RNA-Seq theory and workflow
- Gene expression quantification and differential gene expression analysis
- MicroRNA target prediction and analysis
- Introduction to Single-Cell Analysis
- Pre-processing of 10X scRNA Datasets
- Clustering 3K PBMCs with ScanPy
- Understanding Barcodes
- Custom pre-processing of scRNA
Learning Goals:
The purpose of this workshop is to gain knowledge on Next Generation Sequencing (NGS) with a special focus on bulk and single-cell RNA-Seq data analysis in Arabidopsis thaliana. Although it is designed to deal with plant transcriptome data analysis, most of the analysis can be adapted to other organisms too.
Prerequisites:
The target audience includes biologists and researchers interested in bulk and single-cell RNA-Seq data analysis. Specifically, we encourage scholars that have begun biological data analysis and are interested to know what RNA-Seq analysis is and how they can use Galaxy for RNA-seq data analysis. Different datasets will be used during this workshop and the audience will learn universal tools, workflows and a framework applicable to different domains.
Keywords:
Galaxy, Machine Learning, Docker, Galaxy Flavors, Interactive Tours, Transcriptomics, Data formatting
Tools:
Galaxy (https://usegalaxy.eu)
Contact:
Registration:
https://docs.google.com/document/d/1Y5MqYmMxFCy7PDImYYuHLhgCKVV7MjoGMr22G2U68Ec/preview