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IS any one using Bioperl Coordinate Genemap to Map between cDNA coordiantes vs Gene(Genome) Coordinates? Can it be done in that module and any example ? Thanks,
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I used that module once and it is designed to do things exactly like you want. I was doing something slightly different, taking genomic coordinates of SNPs, converting to CDS then to codon to determine the SNP was synonymous or not. The documentation is very sketchy, and I never got it to work entirely. It would work if the SNP was in the first exon but not if it was in a later exon. I can't say for sure whether this was due to a bug in the module or if I had not implemented it properly. Since I had only a small number of SNPs to check I soon gave up and "did it by hand".
I hope I'm not discouraging you from trying this module. As I said it is designed to do exactly what you want. If you can work with it that would be great.
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