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Old 09-09-2017, 12:35 AM   #1
guesswhat
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Unhappy MiSeq v3 (2X300PE) 16S sequencing, no values for clusters PF

We recently have problems with 16S runs. We have been following the illumina protocol for v3-v4 regions, but have difficulties to get the optimum cluster density and >Q30 values.

We multiplexed 96 samples with Nextera XT v2 set A. Loaded 4pM lib+20% 4pM PhiX.

Now we see another problem, after 25 cycles there was values for cluster density 507K/mm2, but no values for Clusters PF and >Q30.

Is there anyone had the same problem? There was no error or warning message, the run is still going on.
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Old 09-11-2017, 03:07 AM   #2
guesswhat
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I got reply from Illumina tech support. They said that the MiSeq control software can be slow at loading data sometimes. My run is finished and PF%, Q30 values turned up at very late stage. In case someone encounter the same problem, just wait patiently :-)
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