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-   -   Agilent human exon coverage plots (http://seqanswers.com/forums/showthread.php?t=11074)

SMO 05-02-2011 11:27 AM

Agilent human exon coverage plots
 
1 Attachment(s)
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?

NextGenSeq 05-02-2011 11:46 AM

How are you sequencing it? GAIIX, HiSeq, SOLdD etc? Barcoded? If so, how many exomes per lane?

SMO 05-02-2011 11:52 AM

These were ran on HiSeq 2000, and were not indexed.

Jon_Keats 05-02-2011 02:44 PM

What are you seeing for percent on target?

SMO 05-03-2011 05:34 AM

on target is around 72-80%.

SMO 05-04-2011 06:18 AM

Also, we are getting an average of 80 million reads for a PE 2x101.

Michael.James.Clark 05-04-2011 02:49 PM

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.

SMO 05-05-2011 05:21 AM

1 Attachment(s)
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.

Michael.James.Clark 05-06-2011 09:39 AM

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. :)

meher 11-25-2012 06:14 AM

Script
 
Quote:

Originally Posted by SMO (Post 40707)
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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