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Old 10-22-2008, 03:26 PM   #1
vruotti
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Default Quality score graph

Just wondering if anyone have seen the same problem with cycle 30.
Thanks,
Victor

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Old 10-23-2008, 01:21 AM   #2
new300
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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?
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Old 11-06-2008, 09:25 PM   #3
glacerda
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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.

[]s
glacerda
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Old 11-20-2008, 02:06 PM   #4
TylerBackman
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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.
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