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Old 10-14-2013, 06:59 PM   #1
achon
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Location: USA

Join Date: Jun 2010
Posts: 1
Default Truseq: insert size <100bp complications

Hello community,
I currently have a designed custom amplicon panel with insert sizes around 100bp which for the most part work fine. I'm noticing some variability in that the longer insert sizes seem to have a consistently higher coverage than the shorter ones (lower vs upper quartile). Unfortunately qPCR and dPCR are not options due to the size of the panel.

Platform: MiSeq
Kit/Adapters: TruSeq

Before I redesign my primers, any advice? Is it possible to reliably reduce the insert size to ~50bp or lower and if so, what complications or design considerations are there? I've already lengthened the primer+adapters to somewhat already diminished fragment size.
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