Powered by Precision, Driven by Quality

How to download public SRA Run data

Subscribe To Our Newsletter

Get updates and learn from the best

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 NCBI SRA Toolkit. 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 or ./prefetch -v SRR8434837

fastq-dump –split-files SRR8434837 or ./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

Subscribe To Our Newsletter

Get updates and learn from the best

More To Explore

Genome annotation

The analysis of all bacterial genome starts with genome annotation.  This process can be divided into two steps: Gene-finding step and Functional Annotation step. “Gene-finding”

Share This Post

Share on facebook
Share on linkedin
Share on twitter
Share on email
small_c_popup.png

Have a Question? Let's have a chat?

We're here to answer any question you might have

small_c_popup.png

Have a Question? Let's have a chat?

We're here to answer any question you might have

small_c_popup.png

Stay up to date

Keep up with our latest developments