Today’s we will learn to download FASTQ files from a published paper:
Manuscript: Crotta et al. (2023). Nature Communications. http://doi.org/10.1038/s41467-023-36352-z
STEP 1 : Find where the data is available for download in the above manuscript
Click on the link above and search for “Accession”, “Data availability”, “BioProject ID” or “GEO accession code”
If, only a GEO accession code is available, go to the GEO database and look for BioProject ID - Note, ENA (Step2) requires this identifier to download the data.
Which BioProject ID host the data used in the above manuscript?
STEP 2: Search for data for the identified BioProject ID at the European Nucleotide Archive (ENA) database
Go to https://www.ebi.ac.uk/ena/browser/home and search for the BioProject ID using the search option on the top right corner and click on ‘view’:
STEP3: (if applicable) select one or more BioProject submission(s). Click on the first listed BioProject ID:
STEP4: Select FASTQ files (tick boxes next to the file names) and click on “Get download script”. This will download a bash script (e.g.,
)
Open the downloaded ena file using TextEdit (NotePad or similar app). The downloaded script looks like this:
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039511/SRR1039511_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039520/SRR1039520_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039519/SRR1039519_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039521/SRR1039521_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039520/SRR1039520_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039521/SRR1039521_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039510/SRR1039510_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039510/SRR1039510_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039518/SRR1039518_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007/SRR1039517/SRR1039517_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039509/SRR1039509_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039511/SRR1039511_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039519/SRR1039519_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007/SRR1039517/SRR1039517_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039509/SRR1039509_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039518/SRR1039518_2.fastq.gz
Now using the TextEdit or NotePad app, we will add the following lines to the top of the script - copy and paste the following to the above script:
#!/bin/bash -l #PBS -N nfrnaseq_test #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=24:00:00 #work on current directory (folder) cd $PBS_O_WORKDIR
You should have this:
#!/bin/bash -l #PBS -N nfrnaseq_test #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=24:00:00 #work on current directory (folder) cd $PBS_O_WORKDIR wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039511/SRR1039511_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039520/SRR1039520_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039519/SRR1039519_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039521/SRR1039521_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039520/SRR1039520_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039521/SRR1039521_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039510/SRR1039510_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039510/SRR1039510_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039518/SRR1039518_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007/SRR1039517/SRR1039517_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039509/SRR1039509_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039511/SRR1039511_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039519/SRR1039519_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007/SRR1039517/SRR1039517_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039509/SRR1039509_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039518/SRR1039518_2.fastq.gz
Save the file and now let’s transfer it to the HPC. See below:
NOTE: To proceed, you need to be on QUT’s WiFi network or signed via VPN.
Windows PC: open file finder and type the address below to connect to your home directory in the HPC, and then browse to the /workshop/2024-2/session4_RNAseq/data folder
\\hpc-fs\home\
Mac: open file finder and press “command” + “k” to open prompt, then type the below command, and then browse to the /workshop/2024-2/session4_RNAseq/data folder
smb://hpc-fs/home/
Drag and drop the script into the /workshop/2024-2/session4_RNAseq/data folder
eResearch Downloading public data
ENA Browser
Go to the ENA Browser https://www.ebi.ac.uk/ena/browser/home
Search NGS data of interest
In the ‘view search box' enter one of the following identifiers:
Project accession (i.e., PRJNA229998)
Study accession (i.e., SRP033351)
Experiment accession (i.e., SRX384360)
Run accession (i.e., SRR1039508)
Once there, you can download any associated files by clicking the relevant links and then clicking on “Get download script”.
For example:
wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039510/SRR1039510_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039510/SRR1039510_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039520/SRR1039520_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039520/SRR1039520_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039511/SRR1039511_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039511/SRR1039511_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039521/SRR1039521_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039521/SRR1039521_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007/SRR1039517/SRR1039517_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007/SRR1039517/SRR1039517_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039518/SRR1039518_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039518/SRR1039518_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039509/SRR1039509_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039509/SRR1039509_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039519/SRR1039519_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039519/SRR1039519_2.fastq.gz
Now create a PBS Pro submission script for the above and save it in a file called, for example ‘launch_ENA_download.pbs’. Note: the below script will download the data in the folder from where the script has been sent to the cluster.
#!/bin/bash -l #PBS -N download #PBS -l select=1:ncpus=2:mem=8gb #PBS -l walltime=24:00:00 #work on current directory (folder) cd $PBS_O_WORKDIR wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039510/SRR1039510_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039510/SRR1039510_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039520/SRR1039520_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/000/SRR1039520/SRR1039520_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039511/SRR1039511_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039511/SRR1039511_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039521/SRR1039521_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/001/SRR1039521/SRR1039521_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/004/SRR1039514/SRR1039514_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007/SRR1039517/SRR1039517_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/007/SRR1039517/SRR1039517_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039508/SRR1039508_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039518/SRR1039518_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/008/SRR1039518/SRR1039518_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039509/SRR1039509_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039509/SRR1039509_2.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039519/SRR1039519_1.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103/009/SRR1039519/SRR1039519_2.fastq.gz
Submit the download script to the cluster:
qsub launch_ENA_download.pbs
Monitor progress of job:
qjobs