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Download data using the nf-core/fetchngs pipeline
Source: https://nf-co.re/fetchngs/1.12.0/
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Alternatively, to the above approach we can also use the nextflow nf-core/fetchngs pipeline to download data.
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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:
| 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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