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Old 03-29-2019, 05:51 AM   #1
hoytpr
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Default How to get raw reads from NextSeq

We have used bcl2fastq on our local server for years, but a client has asked for untrimmed unfiltered raw reads. What's the easiest way to get these from a completed run, and still get demultiplexed fastq files? It looks like maybe removing the adapter se1quences from the sample sheet, and set TrimUMI to 0, but I'm not sure how to prevent quality trimming. Do we need a different software than bcl2fastq?

Thanks,
Peter
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Old 03-29-2019, 06:22 AM   #2
GenoMax
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Don't have access to a NextSeq but you may want to look on D drive to see if there is a "NextSeq Analysis" folder. On a MiSeq you can find original full data folder in an analogous spot.
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Old 03-29-2019, 06:37 AM   #3
hoytpr
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Thanks for the reply. These are four runs completed a couple weeks ago, and there are bcl files (e.g. 0001.bcl.ngzf) in four directories
\Data\Intensities\BaseCalls\L001 (through L004). Each .bcl file appears to have an index file associated with it, and there are 91 .bcl.ngcf files for each "Lane".

I can decompress the .bcl.ngzf files to .bcl files, but can't seem to do anything with the index files.
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Old 03-29-2019, 06:58 AM   #4
GenoMax
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My apologies.

I guess you are only asking about how to get data that is not trimmed but still demultiplexed. bcl2fastq would still be the software to use. Remove the adapter sequences from your samplesheet and re-process. I am not sure how this happens on NextSeq (i.e. if it will overwrite the processed data) since we always use bcl2fastq off-line.
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Old 03-29-2019, 07:44 AM   #5
hoytpr
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Thanks. Our analysis is off-line also, so we're re-processing now. Appreciate the reply!
Peter
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