How to download undetermined FASTQ files using BaseSpace CLI

On BaseSpace, all undetermined FASTQ files go to a single project entitled "Unindexed Reads." The user will need to locate the specific App Session ID for the FASTQ Generation associated with the run, in order to download the undetermined FASTQ files from a specific run.

1. To find the App Session ID for the FASTQ generation, navigate to the BaseSpace run summary page and select the FASTQ Generation session for that run.

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1. From the Analysis app session page, copy the App Session ID from the URL.

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1. Next use BaseSpace Command Line Interface (CLI) to perform the following steps:

a. Run the following command with the unique App Session ID, which allows the user to view all of the output datasets associated with the app session (including the undetermined FASTQ datasets):

• bs await appsession [App Session ID]

• (eg, bs await appsession 224334111)

b. In the subsequent output, look for the line that lists the "Undetermined from [Run Name]" and the ID associated (highlighted in image below) with the "Unindexed Reads" project. Copy the ID.

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c. Run the following command to download the datasets, making sure to include a specified output directory, and substitute "[ID]" with the unique ID from step two:

• bs download dataset -i [ID] -o [Output Directory]

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