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Old 05-07-2016, 05:15 AM   #2
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,225
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I wonder which of following you are referring to:

1- whole read was adapter sequence for 20% of reads
2- 3' end of reads had adapter sequence which was 20% of output

The first case indicates incomplete removal of adapters after ligation while the second case would happen if read length were longer than insert size. If you have not use BA then how would you know the average size of libraries which is essential to calculate molar concentration from qPCR results.
PF% is very low which could be result of over clustering among other causes. You need to run sample in BA or a similar device to obtain correct average library size for optimum loading and clustering.

Last edited by nucacidhunter; 05-07-2016 at 12:54 PM. Reason: typo was fixed
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