Sequencing analysis of variants in our Puerto Rican ZIKV stock is now detailed here: https://zika.labkey.com/announcements/OConnor/thread.view?rowId=112 …
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Als antwoord op @pathogenomenick
Thanks for developing the method --it's made sequencing ZIKV much easier.
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I am skeptical that this method is accurate for variant calling - we are running some spike-in controls soon.
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iSNVs you mean? PCR (well, and all amp) methods are somewhat fraught for lower frequency stuff.
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Als antwoord op @pathogenomenick @NathanGrubaugh en
I think particularly when starting molecule # is very low (as per clinical infection) due to stochastic effect
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agreed - i am almost certain that we cannot call iSNVs using an amp method from low titer clinical samples.
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Als antwoord op @NathanGrubaugh @pathogenomenick en
My main issue here is lack of strand-bias correction for AmpSeq. By far most imp. filter.
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Als antwoord op @K_G_Andersen @NathanGrubaugh en
Yes - definitely useful/important. Do you use one?
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Nope - we don't attempt to call iSNVs. Nate's exps will show whether it's even possible.
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