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Old 08-29-2008, 09:51 AM   #1
bioinfosm
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Default 1st cycle report

Hi,

The Solexa first cycle report gives numbers as the cluster count per lane, Intensity and Std dev of A C G Ts, some focus metrics and tilt.

Anything that can be mined out of all these statistics? We are yet to use this report to actually summarize it in words and be able to say something about the quality of run, etc.

Observations?
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Old 08-29-2008, 11:22 AM   #2
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I've worked with the first cycle incorporation reports (.xls) a bit. WikiLIMS uses google charts to turn this


into this


It serves as a visual summary of the A,T,C,G intensities on a per-lane basis. Perhaps that is useful, or will inspire thoughts on what more you'd like distilled.

<blatant ad>I'll be presenting this and much more during Sept 21 in Providence </blatant ad>

Last edited by cariaso; 09-03-2008 at 01:13 PM.
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Old 09-03-2008, 07:51 AM   #3
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Thanks ... anyone else has comments?

I wont be able to make it to RI ... any chance you could post the slides to me?

~sm
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Old 09-03-2008, 08:10 AM   #4
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After they've been delivered I'll update this thread with a google docs url.
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Old 09-09-2008, 07:29 AM   #5
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Quote:
Originally Posted by cariaso View Post
After they've been delivered I'll update this thread with a google docs url.
Awesome.. Thanks!
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Old 09-16-2008, 06:41 AM   #6
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Default IVC.htm plots

Is there a good way to look at the Intensity vs Cycle number plots and say about the tile?

There is an attached image here as an example..
Attached Images
File Type: jpg s_1_0009_all.jpg (9.7 KB, 36 views)
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Old 09-22-2008, 12:46 PM   #7
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Well it seems my fondness for screen shots made this too big for google docs. Truth be told much of the demo was actually live against real systems, instead of being based on the slides. Lastly I didn't provide much text or speaker notes. So I don't know how much value anyone will get from these, but as promised here they are at

http://bioteam.net/cariaso/wikilims-ngs08ri.pdf
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Old 10-02-2008, 07:57 AM   #8
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Thanks !

However, its just that image you have in the slides, any info on the interpretation? how useful is the 1st cycle report info?
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Old 10-07-2008, 12:51 AM   #9
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Its an excellent snapshot for some purposes, lousy for others. At Rhode Island George Grills of Cornell showed some images of QC lane analysis which I believe were generated by intel and I'm now inquiring about over on
http://seqanswers.com/forums/showthread.php?t=630
as for usefulness and interpretation. For the McCombie lab this was the first thing they wanted to know about their data. They had an excel sheet full of numbers, but no intuition on what it meant. This viz addesses that. However it isn't meant for drilldown and deeper analysis, at least until someone tells me what they'd like to know next.
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Old 10-07-2008, 06:35 AM   #10
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Thanks !
Do update in case you get hold of the images, or more interpretation..
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Old 10-09-2008, 11:12 PM   #11
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Default wikilims cshl poster

Since my slides were nearly devoid of text, perhaps this poster will be useful.

http://blog.bioteam.net/2008/10/09/w...ng-conference/
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Old 10-10-2008, 06:13 AM   #12
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Thanks, but the link did not work for me..
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