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Old 11-22-2015, 11:33 AM   #1
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Location: new york

Join Date: Sep 2015
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Default No fastq.gz files from MiSeq

Usually, I could find the two fastq.gz files in the .../Data/Intensitites/BaseCalls folders, but this time, I could not find this two files, although everything else looks normal. Is there a way that I can fast get access to these two files or was it something went wrong?

fabregas is offline   Reply With Quote
Old 11-25-2015, 07:33 AM   #2
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Location: Washington, D.C. metro area

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It's hard to say what went wrong without really looking at your run folder-- were you uploading to basespace and lost a connection (the exact same thing happened to me two weeks ago for exactly that reason)?

Assuming the bcl files are all there, you may just want to generate new fastq files using the bcl2fastq utility. If you're not familiar with bcl2fastq, there's more information on Illumina's website and you can also find a lot of info around here.
Jessica_L is offline   Reply With Quote
Old 11-25-2015, 02:23 PM   #3
Location: Germany

Join Date: Jun 2011
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Do you have access to the MiSeq Reporter? You should be able to access it by opening the browser on your Miseq and typing http://localhost:8042/ in the addressbar bar.
If you have specified "GenerateFASTQ" in your sample file, you should be able to just requeue the run for computation. You can also have a look at the error logs, it may indicate why the initial generation of the fastqs has failed....
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