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Old 02-22-2015, 07:32 AM   #1
Asaf
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Location: Jerusalem

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Unhappy Nextseq500 N's from position 25

Hi,
I've been seeing a lot of Nextseq500 runs lately and I found a very disturbing phenomenon. In a lot of the runs I start seeing a lot of N's from cycle 25 onward. The FastQC looks like this:

This example is extreme but I see it in a lot of cases and it's always from cycle 25.
Any clue?
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Old 02-22-2015, 04:48 PM   #2
GenoMax
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Have you contacted illumina tech support since they are likely going to be able to remotely look at your data and see what could be going wrong.

That said, are these low complexity/amplicon type libraries?
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Old 02-23-2015, 02:52 AM   #3
Asaf
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Quote:
Originally Posted by GenoMax View Post
Have you contacted illumina tech support since they are likely going to be able to remotely look at your data and see what could be going wrong.

That said, are these low complexity/amplicon type libraries?
I didn't try to contact them yet, I'm trying to see if it's common or related to the library construction first. The libraries have a 9 bp barcode and they are bacterial rRNA depleted transcriptomes so they should have good complexity.
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