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Old 12-06-2017, 11:05 AM   #1
Junior Member
Location: Atlanta

Join Date: Dec 2017
Posts: 4
Default OverClustering - MiSeq v2 reagents - Nextera XT Library Prep

Hi everyone,

I am a new user of MiSeq. I am using the Nextera XT Library Prep for sequencing of gDNA along with the MiSeq Reagents v2.

I am having issues with overclustering, and the Q30 was pretty low (58.3%). However, the Cluster Passing Filter % was still around 79%. The images did not look terribly overclustered tough.

I have heard that reviewing parameters on Reads 1, 2, 3 and 4 can help understand what happened but I don't know how to interpret those parameters.
I noticed that for Reads 1 and 4, the Q30 is low : 63%, and 51.6% respectively. However, for Reads 2, and 3, it's pretty good: 90.4%, and 90.8% respectively. What does that mean when the error rates is high for Reads 1 and 4???

Thanks so much for your help!!!!
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