46% reads >Q30 in R2... Why? 😔

[soleulloa]

Hi all,

I've used a MiSeq 500 cycles v2 and 10 pM of my libraries pool + phiX 10%.
Everything was ok but at cycle 491 the run was stopped (I don't know why).
I was looking for some paramethers and that is the information:
1249 mm/k2
R1: 88.16% cluster PF, 85.13% >Q30
R2: 88.16% cluster PF, 46.22% >Q30

Why the quality was so low in R2 sequences? It never ocurrs before ☹️

Thank you!!!
Soledad

[GenoMax]

Take a look at this helpful tech note from Illumina about optimizing cluster densities for various sequencing chemistry/platforms.

Your run is at least borderline over clustered for a V2 run. Once you go past the sweet spot of cluster density for a specific version of chemistry, the cluster density number does not actually reflect reality. If you look at the images from the 485 cycles on you should get an idea of why the run failed. If the images look ok then you should contact Illumina tech support since the run may have suffered a hardware failure.