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Illumina runfolder structure

I sequence my samples with Illumina NovaSeq 6000. When the run finishes, it creates a folder that has a certain structure (aka runfolder), as detailed in this official illumina documentation. For example, in the case of Data\Intensities\BaseCalls\L001\C1.1\L001_1.cbcl,

  • L001 means Lane 1
  • L001_1 means Surface 1 of Lane 1
  • C1 means Circle 1

However, I have yet to be able to understand what ".1" in "C1.1" means? And I can't find any documentation on this.

bcl runfolder illumina bcl2fastq novaseq
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written by scsc185 • scsc185

Are you asking for your own interest or you are planing to do something with the run folder? In practice I'd suggest to let bcl2fastq handle the run folder and work with the resulting fastq files. I'm not sure I've ever come across a situation where I needed the Illumina output upstream of the fastq files.

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written by dariober dariober

This is for my own interest. I do use bcl2fastq.

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written by scsc185 • scsc185

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