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Old 06-02-2014, 06:45 AM   #8
pmiguel
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Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
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Quote:
Originally Posted by nucacidhunter View Post
I have tried logically to explain my observation based on science behind Illumina sequencing system and I do not have any scientific evidence that small and large fragments are involved in flow cell battles for getting sequenced. All sizes of fragments can attach to flow cell lawn and during clustering small fragments will amplify and form denser clusters than large fragments. During template generation RTA passes those pure clusters (resulting from single template strand) with higher intensity which mostly would be smaller fragments clusters. RTA normalises intensities based on all clusters which is relative and in library with large fragments it will pass the ones that have higher intensity too. Looking at thumbnail photos also shows a lot of background clusters which RTA has not picked up for various reasons. I do respect everyone opinion and I am very interested to see scientific explanations.
"Scientific"? What you describe above is a hypothetical. And, yes, I have had Illumina reps tell me the same story. But it does not fit with what I have seen, so I think they are wrong.

You write:
Quote:
Looking at thumbnail photos also shows a lot of background clusters which RTA has not picked up for various reasons.
What is your basis for writing this? I can look at a thumbnail photo, but how do I tell which clusters "RTA has not picked up for various reasons"?

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