fasterq-dump Tutorial: Download FASTQ Files from SRA/NCBI
Introduction
When researchers publish papers that use sequence data from next-generation sequencers, the raw sequence data is typically deposited in a public database. This page walks you through how to retrieve FASTQ files from a public database using the fasterq-dump command included in the SRA Toolkit.
Installing SRA Toolkit
Pre-compiled binaries are available here, so let's go ahead and download them.
Run the following commands to download and extract the archive (example for Mac).
It is recommended to add sratoolkit.*-mac64/bin to your PATH.
We will use fasterq-dump to retrieve FASTQ files, so let's verify the installation by displaying its help message.
If you see output similar to the following, the installation was successful.
Finding an Accession Number
Start by searching for the data you want to download on NCBI SRA. If you already know the accession number, you can skip this step.
Take note of the accession number shown on the screen below.
Downloading FASTQ Files
To download FASTQ files, we use fasterq-dump. There is also an older tool called fastq-dump, but fasterq-dump is its faster replacement.
Run the following command to download the FASTQ file.
When the download is complete, you should see output like this.
"SRR20791120.fastq" has been created in the current directory.
For paired-end reads, use the following option to split the output into separate files.
"SRR20791120_1.fastq" and "SRR20791120_2.fastq" have been created.
RNA-Seq Data Analysis Software
This is an RNA-Seq Data Analysis Software recommended for those who:
✔︎ Seeking to avoid outsourcing or collaboration for RNA-Seq data analysis.
✔︎ Lacking time to learn RNA-Seq data analysis.
✔︎ Frustrated by the complexity of existing tools.
Users can perform gene expression quantification, identification of differentially expressed genes, gene ontology(GO) analysis, pathway analysis, as well as drawing volcano plots, MA plots, and heatmaps.
About the Author
BxINFO LLC
A research support company specializing in bioinformatics.
We provide tools and information to support life science research, with a focus on RNA-Seq analysis.