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Old 04-13-2018, 04:35 AM   #1
JQ.ACGT
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Default Modified seq Illumina Primers for ddRAD

Hello, my ddRAD libraries (mean 550 pb) contain the first 5 identical bases at their ends, belonging to the partial restriction site. They will be paired-end sequenced in a MiSeq. I would like to modify the Illumina sequencing primers by adding those 5 bases at the 3 prime end of each primer. Thus, a higher diversity is expected in the first sequenced bases and also an adequate cluster generation. Does anyone have experience with this approach? and the use or not, and its PhiX concentration. Thank you. Best regards.
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Old 04-13-2018, 06:01 PM   #2
luc
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It could work - however you will not be able to sue the PhiX libraries as spike in since you will can't use the Illumina sequencing primers together with your extended versions.
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Old 04-15-2018, 02:10 AM   #3
JQ.ACGT
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Thank you. It is right. So the question is what can work best. 1) Use modified primers to bypass the restriction site or 2) use a high concentration of PhiX (how much?).
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