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How to download BCL files from NextSeq run?

Hi I'm new to the NGS data analysis, want to practice how to use bcl2fastq to demultiplex a nextseq run.

I have a run from Nextseq few weeks ago (with Basespace, didn't do standalone). Try to download BCL for this run, but I can only download fastq from basespace.illumina.com. I can see the output folder in the basespace, but can only download files one buy one.

My questions are:

1, how to download bulk BCL files from basespace?

2, As I know nextseq only keep the most recent run folder in D:\Illumina\NextSeq Control Software\Temp. But for old runs, if I didn't run standalone , does that means I don't have the output folder in the Nextseq machine, and the output folders are only on Basespace?

Thanks!

sequencing bcl2fastq nextseq
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updated by Biostar Biostar • written by Joe • Joe

1 answer

I can answer my own question now. Use basemount.

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written by Joe • Joe

Old thread, but can you specify how you got to BCL through basemount?

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written by bruce.moran bruce.moran

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