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==Background== *There were a number of differences on the experimental protocols between the two batches of data. **141112_HiSeq: Noi used the Tang et al RRBS method for end-repair and polishing [[Noi/NOTES/2014-10-29]]; capture was done on [[Noi/NOTES/2014-11-4]]; **141216_HiSeq: Noi used the Kapa Hyper Prep kit [[Noi/NOTES/2014-11-30]]; capture was done on [[Noi/NOTES/2014-12-25]] *Noi did the capture experiment: [[Noi/NOTES/2014-12-25]]. *The libraries were sequenced in one HiSeq PE100bp rapid run 141214_SN1001. *Dinh mapped the reads: [[Dinh/Dinh_2015/NOTES/2015-1-7]]. *Dr. Zhang analyzed the Hiseq Rapid run data, mapping rate is good. But specificity and enrichment factors are much lower than the first experiment *Kun did the comparison: [[Kun:LabNotes/MONOD/2015-1-9]]. *Kun did additional comparison for the two sets of data, he is sure the first batch of data has good on-target rates but low library complexity, and the second batch was the opposite. *[[Kun:LabNotes/MONOD/2015-1-9#Further_comparison_of_the_two_batches_of_library_preparation_and_capturing_experiments]]. **Conclusion 1 '''Plasma DNA needs to be end-polished using the standard library prep protocol such as the one implemented in the Kapa Hyper Prep kit'''. **Conclusion 2 '''The Tang et al scRRBS protocol is based on some assumptions of the DNA fragment ends, which are not applicable to all plasma DNA fragments'''. *I just need to repeat the capture experiments on those libraries made in the second batch, then we should be fine. {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8<\hiddentext> |- style="font-size:14pt;font-weight:bold" align="center" | width="74" height="18" | Experiment | width="119" | End Repair | width="53" | Capture | width="66" | Hiseq Run | width="66" | Specificity | width="119" | Enrichment Factors | width="73" | Complexity | width="79" | Clonal Rates | width="528" | Conclusion |- style="font-size:14pt" align="center" | height="18" | #1 | Tang et al RRBS | align="center" | 141104 | align="center" | 141112 |style="background-color:#9BBB59" | higher |style="background-color:#9BBB59" | higher |style="background-color:#DA9694" | lower |style="background-color:#DA9694" | higher | lower complexity and higher clonal rates due to Tang et assumption the DNA fragment ends |- style="font-size:14pt" align="center" | height="18" | #2 | Kapa Hyper Prep kit | align="center" | 141225 | align="center" | 141216 |style="background-color:#DA9694" | lower |style="background-color:#DA9694" | lower |style="background-color:#9BBB59" | higher |style="background-color:#9BBB59" | lower | lower specificity and enrichment due to capture condition |}
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