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Old 05-02-2011, 11:27 AM   #1
SMO
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Default Agilent human exon coverage plots

My lab has been using the Agilent 50Mb SureSelect Human All Exon kit for many months now. Though the data is acceptable, we canít help but wonder why our coverage plots look so different from Agilent coverage plots. (see attachment) Do other users produce data that results in coverage plots similar to those advertised by Agilent? If so, do you have any suggestions as to why we are seeing this disparity? Or, are our results the accepted norm?
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File Type: pdf human coverage plot.pdf (38.6 KB, 206 views)

Last edited by SMO; 05-02-2011 at 11:33 AM.
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Old 05-02-2011, 11:46 AM   #2
NextGenSeq
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How are you sequencing it? GAIIX, HiSeq, SOLdD etc? Barcoded? If so, how many exomes per lane?
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Old 05-02-2011, 11:52 AM   #3
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These were ran on HiSeq 2000, and were not indexed.
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Old 05-02-2011, 02:44 PM   #4
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What are you seeing for percent on target?
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Old 05-03-2011, 05:34 AM   #5
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on target is around 72-80%.

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Old 05-04-2011, 06:18 AM   #6
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Also, we are getting an average of 80 million reads for a PE 2x101.
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Old 05-04-2011, 02:49 PM   #7
Michael.James.Clark
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Your curves are consistent with what I see when running Agilent 50M SureSelect with paired 100bp reads.

Not sure what this "Agilent's data" curve you're showing is, but it may be due to any number of things--library prep, Agilent likely used paired 76bp reads (which they recommend), et cetera.
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Old 05-05-2011, 05:21 AM   #8
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Thanks for the input.
Do you see similar coverage plots for Agilent mouse?
We have noticed that the curves for mouse differ greatly from human, using the same protocol, reagents and technicians. See attachment.
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File Type: pdf Human vs. Mouse.pdf (124.5 KB, 64 views)
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Old 05-06-2011, 09:39 AM   #9
Michael.James.Clark
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I don't understand the Y-axis here. What are you calling "the exome"?

Haven't done Mouse myself. But again, I would not fret over this.

The Sureselect 50M performance is still high over its targets regardless.
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Old 11-25-2012, 06:14 AM   #10
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Quote:
Originally Posted by SMO View Post
My lab has been using the Agilent 50Mb SureSelect Human All Exon kit for many months now. Though the data is acceptable, we canít help but wonder why our coverage plots look so different from Agilent coverage plots. (see attachment) Do other users produce data that results in coverage plots similar to those advertised by Agilent? If so, do you have any suggestions as to why we are seeing this disparity? Or, are our results the accepted norm?
Hi,

could you provide the script, with which you have generated the plot shown in "human coverage plot.pdf" ?
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