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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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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