Galaxy @ ABRF 2020
Single Cell, and Functional Characteristics of Microbiomes
- Date: February 29th 2020- March 3rd 2020
- Location: ABRF 2020, Palm Springs, California, United States
- Contact: Pratik Jagtap
Single cell RNA-seq has recently become a routine experimental tool in biomedical research due to technological advances and its adoption as a service by core facilities. As scRNA-seq technology continues to improve and lead to increasingly complex data, the need for scalable, flexible, and accessible analysis options is critical to researchers. The Galaxy workbench is an analysis environment that provides a diverse array of tool options, scalable data management features, and reproducible workflow execution through an easy to use graphical user interface. Galaxy has been used for genomic data analysis for over a decade and includes many tools required for scRNA-seq analysis. In fact, Galaxy provides a multitude of analysis options, allowing users flexibility in creating, executing, and evaluating the many different scRNA-seq options available in the community. This workshop will introduce users to the Galaxy workbench and scRNA-seq technologies. Participants will perform hands-on guided exercises analyzing and visualizing scRNA-seq dataThis workshop will introduce the Galaxy workbench with guided exercises to familiarize participants with the diverse set of available tools, data management features, collaborative infrastructure, and workflow generation/execution. Participants will also be introduced to scRNA-seq assay technology, analysis and visualization strategies, and examples of scRNA-seq applications. Using guided hands-on exercises, participants will process 10x Genomics scRNA-seq data using workflows to achieve count matrices from raw barcoded reads using workflows in Galaxy. Participants will visualize and interact with processed scRNA-seq data using interactive tools in Galaxy. Have participants share and publish data and workflows to demonstrate collaborative infrastructure. The overall goal of this workshop is to introduce core facility managers and technicians to the Galaxy workbench as an analysis and collaborative platform. generated using the 10x Genomics platform using both of workflow execution and interactive tools.
Functional microbiome analysis which estimates the functional groups expressed by microbial community, enables researchers to look beyond taxonomic composition and correlation with the condition under study. Using microbial community RNASeq data and subsequent metatranscriptomics workflows to elucidate the functional complement of the microbiome is gaining interest in the field. The training workshop will introduce researchers to the basic concepts and tools from the published ASaiM workflow (Batut et al, GigaScience (2018), 7 (6)). Participants will also be able to run workflows on small test datasets. Lastly, workshop trainers will update participants of latest developments in Galaxy tools and workflows for functional microbiome and multi-omics analysis.