Pavankumar Videm, Cristobal Gallardo Alba, Mehmet Tekman (RBC), Anne Fiebig (GCBN), Anton Nekrutenko, Fotis Psomopoulos, Florian Heyl, Peter van Heusden, Amazon Polly, Wendi Bacon

April 19-23, 2021

Online Training

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.

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.

Galaxy, Machine Learning, Docker, Galaxy Flavors, Interactive Tours, Transcriptomics, Data formatting

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