3000/4000 read 2

[GW_OK]

Libraries given above are (in no order) a mix of:
Kapa Hyper Prep, Bioo Scientific Nextflex PCR-free, Illumina Nextera

We've got a Bioo Scientific Nextflex flowcell running now. I'll update once it completes.

Illumina is sending FSE's to pull our entire optics module and check alignments next week. There is hope that it will be less-bad afterwards.

[GenoMax]

We have usual "read2-gate" (like the antenna-gate, bend-gate for new apple products) for a new Illumina technology?

On a serious note, @GW_OK what kind of libraries are represented by these 4 examples?

[Brian Bushnell]

That is consistent with my analysis of data from the HiSeq 4000 platform, provided to us by Illumina. The chemistry (as of a few months ago) was absolutely not up to 2x150bp runs IMO, and read 2 particularly had very low quality. I also analyzed some 2x100bp PhiX data that had decent quality for both read 1 and read 2. So, the platform may be adequate for 2x100bp runs.

[GW_OK]

Anybody here with a 3000/4000 seen poor quality read 2's lately? I have attached example plots from 4 previous runs below. It seems to be library agnostic.

I've been lead to understand that there is an escalating investigation internal to Illumina into possible chemistry issues. They're not comp-ing runs until lot numbers are given for the failed runs, I know that.

Just wondering how far the problem extends.