How Can I Find Out What Assembly Data Is Mapped To?

Question

[Andrea_Bio]

Hello

If i have a set of data for an organism and do not know which assembly it has been mapped to, is there a tool to help me find out.

As an example i have looked at these watson snps here and I cannot tell from looking what assembly they are mapped to and there is nothing in the readme file about the assembly either

thanks

ps: please note this question isn't about the watson snps. They were used as an example. My question is about any tools available to confirm the assembly your data is mapped to.

Answer 1

[Jorge Amigo]

I guess the only way you can make sure about the assembly used is checking it yourself directly. I mean that if you only have a list of SNPs and their positions you can only know their assembly by querying several assemblies (I guess that you're talking about human SNPs, so querying dbSNP129or130-hg18 and dbSNP131or132-hg19 should be enough) and matching them with your SNP position list.

to do so I would use either the UCSC genome browser, as there's an easy way of querying for a list of SNPs against several builds, or even BioMart through their archive system. the problems you may find may go from all SNP positions being the same in one and other build (could happen) to rs numbers being merged from one build to another. I would try that first, as it's easy and fast, and depending on the results I would study any other more complicated options (which, right now, I cannot think of).

Answer 2

[Fred Fleche]

I would guess that the answer is at the top of this file but I am not sure :

ftp://jimwatsonsequence.cshl.edu/00README.releasenotes

[Fred Fleche]

The best way is to use one of the contact referenced in this webpage.

[Andrea_Bio]

how can you be sure that the assembly listed applies to the snp data in the other directory. If you/i suspect it is mapped to NCBI 36 is there a way you can confirm an assembly mapping? That information will be useful to me not just for the snp data but in general

[Andrea_Bio]

how can you be sure that the assembly listed in that readme file applies to data in the other directory? That hapmap data was released 2 years after the snp data (though ncbi36 was around in 2005 before both data files were released). But regardless of this specific data, i was wondering how i could confirm what assembly my data was mapped to if i was unsure.

Answer 3

[Lars Juhl Jensen]

If you look at the genome browser at http://jimwatsonsequence.cshl.edu/ you will see that it is based on NCBI Build 36. This is also the version mentioned at the top of the file that Fred referred to, so it's a pretty good guess that this is the build used for the SNP mapping.

[Andrea_Bio]

i've editted my question. the watson snps were just an example. the main question is about checking an assembly mapping

Answer 4

[Giulietta - Ensembl Helpdesk]

I have to say, I agree with Jorge. There isn't an easy way I know of to determine which assembly you are using. If you have the date that you obtained the information, that may help. You could use Ensembl for this, if a variation is in your list and is also in Ensembl, go to its summary page.

Have a look at the location. Go to the "view in archive site" link at the bottom, and have a look at the coordinates in NCBI36 (the previous assembly), for example in v53. Maybe do this for a few SNPs just to be sure.

Hope this helps.