Hello,
I'm not sure if this is the place to ask this, but if so - here goes. If I have a list of genomic regions (from CNV gains and losses) comprised of chromosome, start and stop (ie. chr7 68000000 71000000) for a given genome build (HG 18), and I want to add the genes (ideally HUGO gene Symbols or refseqIDs)that reside within each region per line. So I want to input something like this: Sample Chromosome Region Event Length JC 507 CD19 chr10:11,997,707-12,330,274 CN Gain 332568 JC 507 CD19 chr10:47,563,503-48,085,608 CN Loss 522106 JC 507 CD19 chr10:69,510,584-69,951,738 CN Gain 441155 And get an output similar to this: Sample Chromosome Region Event Length Gene Symbols JC 507 CD19 chr10:11,997,707-12,330,274 CN Gain 332568 CDC123, DHTKD1, NUDT5, SEC61A2, UPF2 JC 507 CD19 chr10:47,563,503-48,085,608 CN Loss 522106 AGAP9, ANXA8, ANXA8L1, CTSL1P2, FAM25B, FAM25C, FAM25G, GDF10, GDF2, LOC642826, RBP3, ZNF488 JC 507 CD19 chr10:69,510,584-69,951,738 CN Gain 441155 ATOH7, DNA2, HNRNPH3, MYPN, PBLD, RUFY2, SLC25A16 Possible ? Shawn Anderson Application Scientist - Laboratory for Advanced Genome Analysis Vancouver Prostate Centre - Vancouver General Hospital 2660 Oak Street Vancouver BC V6H 3Z6 P:604-875-4111 ext. 63436 F:604-875-5654 [email protected]<mailto:[email protected]> www.LAGAPC.ca<http://www.microarray.prostatecentre.com/>
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