Today’s we will learn to download FASTQ files from a published paper:
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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?
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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’:
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STEP3: (if applicable) select one or more BioProject submission(s). Click on the first listed BioProject ID:
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STEP4: Select FASTQ files of interests and click on “Get “Get download script”script”
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Open the file using TextEdit (NotePad or similar app). The downloaded script looks like this:
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Copy the script to your HPC working folder $HOME/workshop/2024-2/session4_RNAseq/data
See below how to drag and drop the file using File Finder
NOTE: To proceed, you need to be on QUT’s WiFi network or signed via VPN.
To browse the working folder in the HPC type in the file finder:
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First, prepare a file with the list of SRA IDs of interest to be downloaded:
Hint:
In the terminal create a new folder called ‘fetchngs’. For example:
Code Block mkdir $HOME/workshop/2024-2/session4_RNAseq/data/fetchngs #then, move to the newly create folder cd $HOME/workshop/2024-2/session4_RNAseq/data/fetchngs
Copy the following list of IDs. Hint click on the top right corner of the block below to copy the text.
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Alternatively, instead of list of SSR identifiers it is possible to download all data in a given BioProject ID:
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PRJNA862097 |
NOTE: Either the list above or citing the BioProject ID in the ‘ids.csv’ file will download exactly the same data.
Create a ‘ids.csv’. file using nano and paste the list of IDs:
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Next, copy and paste the following PBS script to download the specified files in ‘ids.csv’.
NOTE: instead of listing individual SRR identifiers it is also possible to list the BioProject ID (e.g., PRJNA862107) which will fetch all SRR samples automatically.
Secondly, create a launch PBS script to download the data for the above IDs
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