Refseq Mrna Position To Genomic Position

Question

[Sudeep]

I am trying to find out genomic coordinates for a couple of refseq mrna ids, but a question posted here says that the mapping would be imperfect, but what I see in this file is that the corresponding gene co-ordinates are assigned to refseq ids. This information is really conflicting. Is it okay to carry on and assign the gene co-ordinates to refseq ids since this information is directly from NCBI databases itself ?

[edited part]

What I am trying to do is to see whether it is possible to map dbsnp genomic positions to a corresponding position in the refseq sequence. I know some groups have done it successfully for human, but I am looking for a non model organism (pig to be infact).

Answer 1

[Eric Fournier]

It is true that genomic coordinates are sometimes ambiguous, but that is most often the edge case rather than the norm. The coordinates you will find in the file you linked to are "best guesses", and they're more than likely good enough for your purpose.

Eventually, it boils down to how much uncertainty your analysis can bear, and that is not something we can ascertain unless you give us more information about what you intend to do with these coordinates.

[Sudeep]

Thank you for this clarification, I have edited my question.

[Eric Fournier]

For your given purpose, you can probably go ahead and used mapped coordinates.

Answer 2

[gresserT]

There is a mapping table from UCSC.
http://genome.ucsc.edu/cgi-bin/hgTables

You can download it in the table browser:
http://genome.ucsc.edu/cgi-bin/hgTables