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Hi,
I am creating my mapping file and I have a doubt. I have the Fusion (Linker) +Key+Barcode+Primer and then in the reverse primer I have Fusion (Linker)+Key+Primer. So does the linker primer sequence mean the entire one without the barcode or just the Linker alone? Please help.
Thanks,
Lekha
Jai Ram Rideout
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Aug 17, 2016, 1:36:33 PM8/17/16
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Hi Lekha,
I've contacted a developer to help answer your question.
Best,
Jai
TonyWalters
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Aug 17, 2016, 3:03:18 PM8/17/16
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Hello,
The linker you are describing is different than the linker that is part of the LinkerPrimerSequence value. It usually is just 2 nucleotides, and sits between the barcode and the primer. I would just put everything after (3' direction) the barcode portion of your construct under the LinkerPrimerSequence field. For the ReversePrimer, I would just do the primer component.
-Tony
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TonyWalters
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Aug 17, 2016, 10:57:33 PM8/17/16
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Hello Lekha,
That should be fine, since this line is zero: Percent of sequences with barcodes detected at the beginning of the sequence: 0.000 It looks like there are some small fraction of the reads that happen to have one of the sequences matching your barcode *somewhere* within the read itself, which can happen with short sequences like the barcode.