2 minute read

In this post, I will detail how to download some raw sequence data from GEO/SRA in fastq format.

We will be using data from the following publication as an example: Rauch A, Haakonsson AK, Madsen JGS, Larsen M et al. Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis. Nat Genet 2019 Apr;51(4):716-727. PMID: 30833796

The data was deposited at GEO/SRA and is accessible through the GEO data set GSE113253. You can further link to the relevant SRP SRP140638

Typically, this will be performed using High Performance Computing (HPC) with Platform Load Sharing Facility (or simply LSF), which is a workload management platform, job scheduler, for distributed high performance computing. Your HPC should have most of the modules needed installed for you already. If not, then please find the related-links below.

The SRA toolkit

Finding the SRA

For example, to get fastq files for the sample:GSM3405962: RNA-seq, SHSY5Y adipocyte diff 7d; Homo sapiens; RNA-Seq, you would go to the SRP linked above.

Go to the corresponding SRA page: https://www.ncbi.nlm.nih.gov/sra/SRX4774806[accn]

Copy down the appropriate Accession: SRR7939701

Downloading the data

Type the following into the command line to begin downloading your data:

prefetch -v SRR7939701

If you wanted to download multiple files, it is recommended to use the RunSelector. On the SRP page, you should see a link at the top for Send results to Run selector.

Here select the samples or Runs that you want to download by clicking on the appropriate checkboxes. Then download the Accession List and the Metadata if needed.

Depending on the naming convention or format of the Accession List, you can download all of the Runs with the following:

prefetch $(<SRA_Acc_List.txt)

Make sure you know where the files will be downloaded to or set it up in the options.

Converting to FASTQ

I use the following bash script for converting multiple SRA to fastq. The script will search through my SRA directory for .SRA files and provide these files as the input for fasterq-dump

#fasterq-dump script
module load sratoolkit/2.9.4
module load parallel
#find directory
find $SCRATCH/opt/sra/*sra | parallel 'fasterq-dump -O $SCRATCH/opt/fastq {}'

If you have only one file, then just simply type the following the command line:

fasterq-dump SRR7939701

In another post, I will detail how to align the FASTQ to a reference genome.