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Old 10-29-2018, 12:10 PM   #1
Chris Coldren
Junior Member
Location: Nashville TN

Join Date: Oct 2018
Posts: 1
Default Bubbles in R1 only (NextSeq500)

Hi seqanswers! We have a new problem with our NextSeq: showers of small bubbles that appear only in R1 and cause high error tiles on the lower surface.

I've attached a plot from IGV. Each of the points above the "usual" error rate curve is an individual tile that has high PhiX error due to the impact of a bubble in the image.

The average error still passes the quoted quality spec, so this obvious flaw hasn't been given full attention by Illumina Tech Support. The interesting factor to me is that the bubbles are completely gone in data R2 (aka R4). We have verified our procedures for thawing and mixing the reagents, and we are concerned that this is a reagent lot-related issue.

Has anyone else seen a similar problem?

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File Type: png nsc347_NS2.png (73.1 KB, 28 views)

Last edited by Chris Coldren; 10-29-2018 at 12:13 PM.
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Old 11-08-2018, 08:47 AM   #2
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Location: Oklahoma

Join Date: Sep 2009
Posts: 411

I'm surprised you haven't had at least one visit from an FSE if this is a recurrent problem. How did you confirm that this was caused by bubbles?
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nextseq, quality

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