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Old 06-02-2014, 06:37 AM   #7
Jafar Jabbari
Location: Melbourne

Join Date: Jan 2013
Posts: 1,238

Nope, as I write above, this does not fit with the actual results we got.
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.

Last edited by nucacidhunter; 06-02-2014 at 07:25 AM.
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