How to select specific runs under the same project ID to download the fastq files

[Mariko T]

Hi all,

 

I have a project, say project A. And I have 5 runs under that project, say run 1-5.

 

What command should I use to download the fastq file for, for example, run 2&3?

 

If I use

.\bs download project /i (A’s id) /o ./Rundata

All the data for the runs 1-5 were downloaded, and it takes a lot of time.

 

Thank you,

Mariko

[Nick Vinckier]

Hi Mariko,

You can do this in 2 steps. The first is where the datasets for a specific run Id are listed, the second is to download those datasets using their Ids:

To get all datasets under a specific run:
bs list dataset --input-run=<RunId>

Then download all those datasets with:

bs download dataset -i <datasetId> -o <output>

A loop of some sort would be helpful to automate that a bit more.

Hope that helps!

Nick

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[Mariko T]

Hi Nick!

Thank you for your reply and it's really helpful.

Would you mind giving me some advice on how to write the script for the 'for' loop command to get all the Biosample data for a run?

Thank you!

Mariko