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Question: rsID from list of chromosome and position
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gravatar for sookwah.yee
4.4 years ago by
sookwah.yee • 0
United States
sookwah.yee • 0 wrote:

Hi,

I wonder could I create a list contain Chromosome number and a column for position (in build 37) and then I can get a output for the rsID using galaxy?  How could i do this?

Thanks.
snp • 2.7k views
ADD COMMENT • link •
modified 4.4 years ago by Bjoern Gruening ♦ 5.1k • written 4.4 years ago by sookwah.yee • 0

Can you please post an example, for me it was not cleat what you want to do. Sorry.

ADD REPLY • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k

Hi,

Thank you.  Please see an example below. I would like to know whether I can use Galaxy or some other source to identify the rsID for the SNP based on chromosome and BP position (build 37).  

Thanks 

CHR    BP

10    71899756
6    109837229
6    109868340
6    109935484
3    61021526
8    29025045
7    141619042
11    87525265
2    179466177
1    82456308
6    35535670
11    87574807
16    18111633
5    5385388
10    54639565
7    128470838
10    113518440
8    6016650

ADD REPLY • link written 4.4 years ago by sookwah.yee • 0
0
gravatar for Bjoern Gruening
4.4 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi,

if you have a file with all rsID you can indeed use Galaxy to filter out the relevant ID's. You should look at the chromosomic region tools, especially the intersect tool. We you have a rsID file with chromosomic regsions you can simply intersect it.

An other possibility would be to merge the chr & pos column and merge both files on that column.  

Hope that helps a little bit and gets you started!

Bjoern
ADD COMMENT • link written 4.4 years ago by Bjoern Gruening ♦ 5.1k
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