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Old 11-14-2014, 12:25 AM   #8
nucacidhunter
Jafar Jabbari
 
Location: Melbourne

Join Date: Jan 2013
Posts: 1,238
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Quote:
Originally Posted by bunce View Post
I would not be so hasty in talking down the contamination risk in amplicon workflows - our ancient DNA set-up is 'extreme' and we still get bleed-though of tags (we never re-use index pairs).
I wonder if you have considered possibility of carry over from a previous run on MiSeq. We use two step PCR and it works well. In addition, it is convenient and we can pool and sequence other libraries as well without risk of unwanted interaction between custom and Illumina sequencing primers. Nano is the most expensive option for Illumina systems per Gb of data.
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