How to download public SRA Run data

How to find public microbiome data based on 16S rRNA gene
09/07/2019
[Quiz] Comparative microbiome analysis
09/19/2019

How to download public SRA Run data

In this tutorial, you will find how to download NCBI SRA Run data. Therefore, I assume that you have SRA Run IDs ready (Run ID starts from SRR*, not SRX or SRE). For how to find these IDs, please visit here.

Install SRA toolkit on your computer

To download any file from the NCBI SRA database, you need to install SRA toolkit software from //www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/. You can install this software on MS Windows, Mac OS X or Linux.

Download using Run IDs

The software is a command-line version. So, you need to start “terminal” program. In the below example, I will use Mac OS X terminal program to download SRR8434837 (a cheese microbiome sample data).

Running two programs subsequently (see below) will download two FASTQ files containing paired-end Illumina raw sequence data targeting 16S rRNA genes with Run ID SRR8434837.

prefetch -v SRR8434837

fastq-dump –split-files SRR8434837

If successful, you will see two files in your directory. You have two files as it is a paired-end data (see here for more details).

SRR8434837_1.fastq & SRR8434837_2.fastq

Mac OS X screen capture. You can do same in other operating systesm.

Now you are ready for uploading these paired-end data into EzBioCloud Microbiome Taxonomic Profiling (MTP) cloud (visit here).


Last updated Sept. 6, 2019