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Old 11-10-2017, 11:05 AM   #1
kcolt
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Location: San Diego

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Question NextSeq - Banded Clustering images

In September, I noticed that our NextSeq is producing a very odd banded clustering image. Specifically a there's a very bright band of clusters through the middle ~1/5th, and dark, more sparse clusters on the top and bottom. The Illumina rep sent a tech to clean the cameras, but the issue is now still happening.

Our latest run gave okay run stats (a little worse than I'd expect based on the cluster density), but ~50% of the samples dropped out after quality filtering (after about 50-70bp the quality dips significantly). I've contacted them again this week but they are saying that the banded imaging is not unusual, and because the run is still technically above their quality metrics there's nothing wrong.

Has anyone experienced this banded clustering? Is there a cause for this?

Perhaps there are two separate unrelated things happening, the bands and the quality drop-off?
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Old 11-10-2017, 04:37 PM   #2
kcolt
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Found how to attach images
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File Type: jpg 1087-clustering.JPG (97.2 KB, 17 views)
File Type: jpg bands.JPG (45.3 KB, 17 views)
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cluster density, cluster formation, nextseq, nextseq500, quality filtering

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