slight over clustering?

[ox_zoo]

Hello,

I have, this morning, set up a Next-Seq run for some ChIP-seq libraries. It is now on its 39th cycle. However, the cluster PF value is 75.94 yet the %≥Q30 is at 90.82. I have around 150,000,000 reads per lane...


I was wondering is this a case of over-clustering? If so, are the reads not as usable?

[nucacidhunter]

With those read numbers it has over clustered. Q30 score for that cycle is lower than scores for a standard run. You will expect that Q score will fall lower as the cycles number increases.

Reads would be usable and depending on downstream application more or less trimming would be required.

[jdk787]

Also, if the NextSeq is like other Illumina machines your index read quality will be affected more negatively than the R1 and R2 reads. This can cause a loss of data from unidentifiable indices during demultiplexing.