e-learning
SRA Aligned Read Format to Speed Up SARS-CoV-2 data Analysis
Abstract
Traditionally, after a list of run accessions has been filtered on the NCBI website, the accessions are used to download and extract fastq using the SRA toolkit to enter into the next steps of the workflow. A newer compressed data type, generated from raw submitted data containing SARS-CoV-2 sequence, is also accessible to Galaxy users from SRA in the Cloud.
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
- How can I search SRA SARS-CoV-2 metadata from within Galaxy?
- How can I import SRA aligned read files and extract the data in my format of choice?
- How can I import vcf files into Galaxy that have been generated for these Runs?
Learning Objectives
- Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content
- Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format
Licence: Creative Commons Attribution 4.0 International
Keywords: Using Galaxy and Managing your Data, covid19, ncbi
Target audience: Students
Resource type: e-learning
Version: 12
Status: Active
Prerequisites:
Rule Based Uploader
Learning objectives:
- Learn about SRA aligned read format and vcf files for Runs containing SARS-CoV-2 content
- Understand how to search the metadata for these Runs to find your dataset of interest and then import that data in your preferred format
Date modified: 2024-06-14
Date published: 2021-05-31
Contributors: Björn Grüning, Helena Rasche, Mehmet Tekman, Nate Coraor, Saskia Hiltemann
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