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.
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.
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
Now you are ready for uploading these paired-end data into EzBioCloud Microbiome Taxonomic Profiling (MTP) cloud (visit here).
Last updated Sept. 6, 2019