[Quiz] Comparative microbiome analysis

How to download public SRA Run data
09/07/2019

[Quiz] Comparative microbiome analysis

In this practical class, students will learn how to analyze the microbiome data using real data. Students are expected to learn:

  • How to search the literature and next-generation sequencing(NGS) database
  • How to download NGS data
  • How to analyze taxonomic profiles of microbiome data
  • How to compare two groups of microbiome data
  • How to test the hypothesis

Please the following steps:

1. Set up your hypothesis or research questions

Our goal is to compare two groups of microbiome data. You can compare any data if data is available for downloading from public data. Fortunately, data of >100,000 microbiome samples are readily available. Therefore, you have a chance to set up a variety of hypothesis and research questions which may not be done before by any microbiologists.

Below are some examples, but you may come up with a brilliant idea of your own:

  • What are the bacterial compositions of dog and cat? What are the differentially present bacterial species, called biomarkers, between two animal species?
  • What are the bacterial compositions of the healthy and diseased? It can be any disease, including obesity, diabetes, Crohn’s disease, cancer, etc. What are the differentially present bacterial species, called biomarkers, between the healthy and diseased patients?
  •  What are the bacterial compositions of the seawater and river water? What are the differentially present bacterial species, called biomarkers, between two environments?

2. Find the NGS data for your study.

If you cannot find them, you need to re-setup your research question. Consult this document for how to search and secure SRA Run accessions. The 10 samples per group is recommended.

3. Download NGS data from SRA database

Once you find the SRA Run accessions (SRR*), you are ready for download. Please follow this document.

4. Upload the paired-end NGS data files

Create an account at EzBioCloud.net. Start upload data (FASTQ files) by following this instruction.

5. Analyze data and generate a research paper.

A tutorial is available for familiarize yourself with the EzBioCloud system. Please follow this tutorial.