[DRYTCYV]

Illumina currently has serious problems with MiSeq V2 and V3 reagents... Some lots perform terribly bad. Others are fine. It seems they are not communicating that well. I guess this is a problem particularly for smaller labs with lower throughput. Maybe it would be useful if we would come up with a shared spreadsheet where bad lots are identified?

Hi Vinz,

Thank you for your post.
It was me that opened this discussion about the contamination, just because we detected some biofilm in the manual sipper. And after the new non-official bleach wash (tech support) we had the worst Q30 in R2 ~50. I said maybe its correlated with this new wash protocol (all lines dilution 1:100 bleach) and then 2 maintenance just with water. In the end just because we had a cluster density of 1480, they simply don't give any feedback.
When we talk with tech support or the problem is low diversity or high clustering that affect everything.......
We are running RAD experiments with low diversity and a clustering of 1700 and very good results

But the idea of problematic lots is good!

Cheers,

[Vinz]

Indeed the support usually stops thinking if cluster density is high. Our experience is that the MiSeqs are pretty robust with regard to overclustering and usually the problem lies elsewhere. However, 1500 is pretty high and I would not exclude that it may interefere...