demuxed read structure

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daniel...@gmail.com

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Apr 27, 2020, 5:41:01 PM4/27/20
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Hi all,
Understandin lab protocols is not my strong suite. Would you be able to describe what the single, 75 bp read structure looks like?

For (wildly fictional) example:
1-12 barcode 1
13-25 barcode 2
26-50 Orf1ab gene target
51-62 barcode 2 reverse
63-75 barcode reverse

This would give me a better sense of the analysis that needs to be done. 

Thanks in advance.
Daniel

Aaron H

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Apr 27, 2020, 5:58:04 PM4/27/20
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Hi Daniel,

Check out figure 1F, a 75 bp sequencing output will start with the Fwd primer and go halfway through the second half of the FIP primer.

Aaron

daniel...@gmail.com

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Apr 28, 2020, 12:45:07 PM4/28/20
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Thanks Aaron - I didn't realize the figure was actually 75 bp long- thought it was more conceptual..

Aaron H

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Apr 28, 2020, 1:01:19 PM4/28/20
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The whole sequence is 120bp and if someone did longer reads, they could get both virus regions but I don't think the impact on turn around time is worth it.
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