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Just wondering if anyone have seen the same problem with cycle 30.
Thanks,
Victor
Thanks,
Victor
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it's not normal. This is for a single run? If you have the images look at the images, see if they get dimmer or something else strange happens at cycle 30. If you don't have the images then look at the intensity plots, do you have a significant drop in average intensity around cycle 30? What do the error rates for cycle 30+ look like on the control lane? -
This is Solexa, right?
If it is, maybe you would like to look at that
maybe you would like to look at that:
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. 2008, July. Nucl. Acids Res.
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glacerdaComment
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I already posted this answer in the other thread where you asked about this, but I thought I'd post it here as well. This is possibly an artifact of the Illumina pipeline quality score normalization rather than an actual sudden drop in quality.
This is most likely because the qualities you are looking at are alignment normalized, and a large number of your sequences failed to align to the reference genome (due to a ligated adapter, etc.)
Take a look at the un-normalized scores (s_<lane>_qraw.txt) instead, I think you'll find that the curve is more continuous between cycles.@1
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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