How-to: download data from SRA


Using SRA toolkit

Install sratoolkit

wget ""
tar -xzf sratoolkit.current-centos_linux64.tar.gz


./vdb-config -i

Follow the instructions to change the download directory. The tools will download the data into /ncbi/public/sra/, wherever you have it set. When downloading protected data such as GTEx, you will need a project key (prj_XXXX.ngc) and to configure the toolkit to use it.

Download a sample as an SRA file

prefetch SRR3485764
fastq-dump –split-files /ncbi/public/sra/SRR3485764.sra 

Download a sample as a fastq file

fastq-dump –split-files SRR3485764 

Note, this still downloads the .sra file first.

Using aspera connect

Install aspera

sh aspera-connect-[version].sh

Download file

ascp -QT -l 300m -P33001 -i <aspera connect installation directory>/etc/asperaweb_id_dsa.openssh<file or files to download> <download location>

FTP from ENA

wget “*”
Senior Lecturer

My research interests include functional genomics, transcriptomics, X-linked disorders, sex differences in disease, X-inactivation and skewing, and meta-analysis.