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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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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