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Old 12-28-2016, 07:05 AM   #1
LUR
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Location: Milan

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Default low fluorescence intensities read 2, HiSeq 2000

hi everyone
I have a problem with PE module Hiseq 2000
Basically the instrument read well the read 1 and the read index, but when arrive to the read 2, the fluorescence intensities are very low and sometime with Q30 around 0 (RNAseq libraries read at 50 PE).
I have opened a case with Illumina 2 month ago but I haven't the solution yet.
Someone have had the same problem?

Thanks a lot
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Old 01-03-2017, 11:37 AM   #2
pmiguel
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Default

Well, unless you are using crazy old single read Illumina adapters, it sounds like something went awry during turn-around.
If you are under a service contract you should ask Illumina to replace the reagents so you can give it another shot.

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Phillip
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Old 01-04-2017, 05:54 AM   #3
helskel
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Default Have you checked your NaOH?

It is also possible that you have an issue with the NaOH. If the concentration of your NaOH in the PE module is off, you will not get through turnaround efficiently, and that can lead to all of the issues that you described.
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fluorescence, hiseq 2000, low intensity, paired end reads

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