Setup SRA Toolkit on the Linux

Setting up SRA Toolkit on Ubuntu

Downloading SRA Toolkit:

1. To download the current version of SRA Toolkit on your Linux, go to:

   http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/current/sratoolkit.current-ubuntu64.tar.gz
   

2. Extract the tar file on your desktop
   tar -vxzf sratoolkit.tar.gz

Two ways of running SRA Toolkit on Linux

By setting up PATH variable

In your terminal, type
export PATH=$PATH:$PWD/sratoolkit.2.4.0-1.mac64/bin

Then, you could check if it is in the PATH variable by

echo $PATH which fastq-dump

By visiting SRA toolkit directory

cd sratoolkit.2.8.2-1-ubuntu64/bin

Testing SRA Toolkit

You could check if SRA Toolkit is currently working on your Linux by

fastq-dump --stdout SRR390728 | head -n 8

It should give you an output exactly like this:

@SRR390728.1 1 length=72 CATTCTTCACGTAGTTCTCGAGCCTTGGTTTTCAGCGATGGAGAATGACTTTGACAAGCTGAGAGAAGNTNC
+SRR390728.1 1 length=72
;;;;;;;;;;;;;;;;;;;;;;;;;;;9;;665142;;;;;;;;;;;;;;;;;;;;;;;;;;;;;96&&&&(
@SRR390728.2 2 length=72 AAGTAGGTCTCGTCTGTGTTTTCTACGAGCTTGTGTTCCAGCTGACCCACTCCCTGGGTGGGGGGACTGGGT
+SRR390728.2 2 length=72
;;;;;;;;;;;;;;;;;4;;;;3;393.1+4&&5&&;;;;;;;;;;;;;;;;;;;;;<9;<;;;;;464262

Downloading RNAseq Data from SRA Database

1. Go to https://www.ncbi.nlm.nih.gov/sra/
2. Search for specific species name (e.g. fundulus heteroclitus)
3. Click the one you would like to download
4. Find the RUN# (e.g. SRR4431245) and write down this number
5. On terminal,
   fastq-dump SRR4431245
   Then, the data should be downloaded to your current directory automatically.

Acknowledgements

This document is modified based on the Wiki page of NCBI GitHub site (https://github.com/ncbi/sra-tools/wiki)