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-   -   primer-dimer or adaptor-dimer (http://seqanswers.com/forums/showthread.php?t=81138)

woodyzc 03-09-2018 10:17 AM

primer-dimer or adaptor-dimer
 
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Hi, all,
I just prepared couple of libraries with the NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina. After run them on a Qiaxcel system, I saw a visible ~35bp peak.(15bp and 3000bp are alignment markers) Could it be primer-dimer or adaptor-dimer? Should I perform another round of beads clean-up? Or I can just send them for sequencing?
Thank

jwfoley 03-09-2018 12:47 PM

No, that's just primer. An adapter dimer would be ~120 bp long. This isn't long enough to contain both adapters so it won't cluster on a flow cell and therefore shouldn't affect anything.

pmiguel 03-13-2018 12:51 PM

I agree with jwfoley.
Unless you were going to have them sequenced on a patterned flowcell instrument (HiSeq 3000/4000/X, NovaSeq) -- then you want another ampure because extra adapter oligos are said to potentiate index hopping.

--
Phillip

seq198 04-25-2018 05:04 AM

You may also try to use less primers in your index PCR


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