I know only a little about Illumina's sequencing. Is it possible to use custom primers in Illumina's flow channel? Anybody know how their primer is attached to the polyacrylamide coating?
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It isn't too hard. It's best to just make your oligos as similar as possible to Illumina's own. You should probably refer to this earlier thread on how to design the primers and adapters:
http://seqanswers.com/forums/showthread.php?t=198
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