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Old 03-09-2018, 10:17 AM   #1
woodyzc
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Default primer-dimer or adaptor-dimer

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?
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Old 03-09-2018, 12:47 PM   #2
jwfoley
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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.
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Old 03-13-2018, 12:51 PM   #3
pmiguel
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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.

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Old 04-25-2018, 05:04 AM   #4
seq198
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You may also try to use less primers in your index PCR
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