Fetching Public RNA-seq data
Manuscript: Crotta et al. (2023). Nature Communications. http://doi.org/10.1038/s41467-023-36352-z
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Find where the data is available for download in the above manuscript.
Hints:
Search for “Data availability” or reference to “BioProject ID” or “GEO accession code”
Find the BioProject ID and search for this ID at https://www.ebi.ac.uk/ena/browser/home
Select FASTQ files of interests and click on “Get download script”
Copy the downloaded file to your HPC account or copy the content to a file created in the HPC using Nano (or other text editor)
Add the PBS pro scheduler lines and submit a job. See step by step details at:
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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/rnaseqsession4_RNAseq/data/fetchngs #then, move to the newly create folder cd $HOME/workshop/2024-2/rnaseqsession4_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:
| Code Block |
|---|
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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