[HMorrison]

Bubbles not BMS

You picture is a bubble, it looks like, not exactly killing your entire swath. I've got bubbles like that for sure, but it's not the dreaded BM(LR)S.

Okay, I'm conflating the two problems, sorry. I should call it something else. But they're frequent, big, and move during the run so we lose lots of data. What *is* the solution? Apparently degassing reagents is not advised.

[HMorrison]

Swath dropout

Here's the swath dropout picture. Top middle. Also occurred on bottom middle.

[GW_OK]

Here's the swath dropout picture. Top middle. Also occurred on bottom middle.

Yep, that's a swath loss. And I did try degassing the scan mix once but it didn't seem to do anything to lessen the bubbles. The bubbles aren't the end of the world, though, at worst you'll have an N in your sequence. And since degassing didn't seem to do much I'm at a bit of a loss as to how to combat it as well.

[HMorrison]

Current run...top middle and bottom middle swath dropout on lane 4 at cycles 17, 38, 40, 52, 57, 58 and counting. Haven't checked other lanes. Ns in sequences hurt; we are doing 16s tag analysis as well as genomic/metagenomic libraries.

[GW_OK]

Dang, that is a ton of dropouts. I hope Illumina is comp-ing you kits.

[HMorrison]

Dang, that is a ton of dropouts. I hope Illumina is comp-ing you kits.

We'd rather have one decent run. As I said, I think we have a lemon of an instrument. With Roche, it's poor reagent QC; with Illumina, the instrument; with IonTorrent, high error. Longing for the old capillary sequencing days (although I go back to Maxam and Gilbert, personally).

[GW_OK]

We'd rather have one decent run. As I said, I think we have a lemon of an instrument. With Roche, it's poor reagent QC; with Illumina, the instrument; with IonTorrent, high error. Longing for the old capillary sequencing days (although I go back to Maxam and Gilbert, personally).

Eh, machines are machines. Back when I was feeding 14 3700's there always seemed to be something going wrong with one of them.

It does sound like you have something bad somewhere in there.