Today’s we will learn to download FASTQ files from a published paper:
Manuscript: Crotta et al. (2023). Repair of airway epithelia requires metabolic rewiring towards fatty acid oxidation. Nature Communications. http://doi.org/10.1038/s41467-023-36352-z
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Click on the link above and search for “Accession”“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?
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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.,
)View file name ena-file-download-selected-files-20241009-0005.sh
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STEP 5: Open the downloaded ena file using TextEdit (NotePad or similar app). The downloaded script looks like this:
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wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/001044/SRR1039511SRR20630344/SRR1039511_2SRR20630344.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/000049/SRR1039520SRR20630349/SRR1039520_2SRR20630349.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/009055/SRR1039519SRR20630355/SRR1039519_2SRR20630355.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/004047/SRR1039514SRR20630347/SRR1039514_1SRR20630347.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/001050/SRR1039521SRR20630350/SRR1039521_2SRR20630350.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/000042/SRR1039520SRR20630342/SRR1039520_1SRR20630342.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/001053/SRR1039521SRR20630353/SRR1039521_1SRR20630353.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/000043/SRR1039510SRR20630343/SRR1039510_2SRR20630343.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/008039/SRR1039508SRR20630339/SRR1039508_1SRR20630339.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/000056/SRR1039510SRR20630356/SRR1039510_1SRR20630356.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/008054/SRR1039518SRR20630354/SRR1039518_1SRR20630354.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/007041/SRR1039517SRR20630341/SRR1039517_1SRR20630341.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/009045/SRR1039509SRR20630345/SRR1039509_1SRR20630345.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/004051/SRR1039514SRR20630351/SRR1039514_2SRR20630351.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/001040/SRR1039511SRR20630340/SRR1039511_1SRR20630340.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/009048/SRR1039519SRR20630348/SRR1039519_1SRR20630348.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/007052/SRR1039517SRR20630352/SRR1039517_2SRR20630352.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/008046/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_2SRR20630346/SRR20630346.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:
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#!/bin/bash -l #PBS -N nfrnaseqENA_data_testdownload #PBS -l select=1:ncpus=2:mem=4gb #PBS -l walltime=24:00:00 #work on current directory (folder) cd $PBS_O_WORKDIR |
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#!/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/SRR103SRR206/001044/SRR1039511SRR20630344/SRR1039511_2SRR20630344.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/000049/SRR1039520SRR20630349/SRR1039520_2SRR20630349.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/009055/SRR1039519SRR20630355/SRR1039519_2SRR20630355.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/004047/SRR1039514SRR20630347/SRR1039514_1SRR20630347.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/001050/SRR1039521SRR20630350/SRR1039521_2SRR20630350.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/000042/SRR1039520SRR20630342/SRR1039520_1SRR20630342.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/001053/SRR1039521SRR20630353/SRR1039521_1SRR20630353.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/000043/SRR1039510SRR20630343/SRR1039510_2SRR20630343.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/008039/SRR1039508SRR20630339/SRR1039508_1SRR20630339.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/000056/SRR1039510SRR20630356/SRR1039510_1SRR20630356.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/008054/SRR1039518SRR20630354/SRR1039518_1SRR20630354.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/007041/SRR1039517SRR20630341/SRR1039517_1SRR20630341.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/009045/SRR1039509SRR20630345/SRR1039509_1SRR20630345.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/004051/SRR1039514SRR20630351/SRR1039514_2SRR20630351.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/001040/SRR1039511SRR20630340/SRR1039511_1SRR20630340.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/009048/SRR1039519SRR20630348/SRR1039519_1SRR20630348.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/007052/SRR1039517SRR20630352/SRR1039517_2SRR20630352.fastq.gz wget -nc ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR103SRR206/008046/SRR1039508SRR20630346/SRR1039508_2SRR20630346.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 |
STEP 6: 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/mydata folder
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\\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/mydata folder
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smb://hpc-fs/home/ |
Drag and drop the script into the /workshop/2024-2/session4_RNAseq/data/mydata 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:
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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.
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#!/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:
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STEP 7: We will ensure the copied file from our laptop / desktop does not have unwanted characters. Let’s move to the data folder:
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cd $HOME/workshop/2024-2/session4_RNAseq/data/mydata |
How to use the dos2unix tool? Type:
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dos2unix --help |
Now let’s run dos2unix conversion. Note the filename may vary, so adjust the filename as appropriate.
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dos2unix -n ena-file-download-selected-files-20241013-1123.sh ena-file-download-selected-files-20241013-1123.pbs |
Note: If you create a file using Microsoft Excel, it is likely that it will add ASCII characters, use dos2unix to remove such characters.
Now we are ready to submit to the HPC cluster the script to download FASTQ files:
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qsub ena-file-download-selected-files-20241013-1123.pbs |
Monitor progress of job:
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qjobs |
Note: Downloading the above datasets will take about ~50 minutes.
Find in the link below alternative approaches to download data from SRA, BaseSpace or use the nf-core/fetchngs pipeline: