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==Probe design Version 2== I came up with an iterative primer searching program when working on the design of CpG island probes. I decided to modify this program for exonome probe design since it will generate probes for many regions that were missing by Keith's program. Here is the [[Media:getExonicPrimers.txt|code of my program]]. The gap for fill-ins is 175-225bp. I was able to design 381,765 probes covering 183,448 exons in the human RefSeq genes. The total length of exonic sequences captured is 80,719,171bps. The total non-overlapping genomic regions covered by this probe set is 68,730,151bps. I selected a subset of 55,067 probes targeting the first 3760 genes in the Cosmic gene database. The last 67 probes were removed to make a 55k set. This is the second 55k exonic chip synthesized at Agilent, called Cosmic3760 library. I used the V4 adaptors and the V7 linker. The reason of using V4 adaptor is to have the option of using BciVI. *[[Media:ECosmic3760_probes.txt.gz|Probe information file.]] *[[Media:Cosmic3760.seq.gz|Raw sequences of all 55,000 probes.]]
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