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How to download FASTQs from specific lanes using Basespace CLI

Basespace CLI can be used to do download FASTQ files from specific lanes with the following command:
bs download project -i [projectID] -o /output/directory --extension=fastq.gz --exclude '\*' --include '\L00#\'
where # is the desired lane
If more than one lane is desired, add a second "--include" section following the first one:
bs download project -i [projectID] -o /output/directory --extension=fastq.gz --exclude '\*' --include '\L00#\' --include '\L00#\'
For any feedback or questions regarding this article (Illumina Knowledge Article #6973), contact Illumina Technical Support [email protected].
Last modified 25d ago
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