Region Reference (And Alternate) Alleles By Columns

Question

[Ryan D]

Hi there, suppose we want to get reference and alternate alleles for several regions of the genome. Is there a way to do this from UCSC Table Browser or Galaxy?

We're looking to get a format like this

chr1 100000 G G
chr1 100001 G G
...
chr1 100007 C C
chr1 100008 A A
chr1 100009 A T rs123

In other words every chromosome, base pair, reference, and, if applicable, alternate alleles and SNPs in columns. Strand orientation (if not already positive) would be great. Any help is appreciated? 5000.

Answer 1

[Treylathe]

If I understand the question, this should be a simple table browser search.

• Choose the necessary genome assembly.
• Choose the desired dbSNP build (131?)
• Then choose the region, locations you are looking for.
• Choose "selected fields..." as your output
• then click "get output"

That should take you to a menu to choose the fields:

I chose location, alleles, function etc and got this:

chr21   33031821    33031822    +   G/T near-gene-5
chr21   33031828    33031829    -   A/C near-gene-5
chr21   33031833    33031834    -   C/G near-gene-5
chr21   33031926    33031927    +   C/G near-gene-5

You could chose IDs, etc to do that.

You could also send that over to Galaxy to rearrange the columns and otherwise manipulate the format and make it what you are looking for:

chr21   33031821 G T +
chr21   33031828 A C -

etc..

Answer 2

[Mary]

I'll just add that if you want defined regions you have to use the box that you get when you click the "defined regions" button instead of doing just a plain genome wide query. Then you enter the regions with the syntax that they show in the example.

[Ryan D]

Right. I know the defined regions box portion, but say I wanted this for all base pairs. So 10001 10002 10003. Realizing that only one in a hundred or so will be SNPs. Thanks both. Let me know if you have a solution for this.

[Treylathe]

so you want a list of all basepairs in a region, whether there is a dbSNP entry for that position or not, but have the dbSNP info too for the positions that do have dbSNP data?

[Treylathe]

off the top of my head, you could get the data above as I suggested, then the same region with a sequence track, export them both to Galaxy and manipulate the columns to the way you want them and then "Join" the two datasets using "all records of both datasets" or from the sequence one? Haven't tested it yet, but might be what you are looking for

[Treylathe]

off the top of my head, you could get the data above as I suggested, then the same region with a sequence track, export them both to Galaxy and manipulate the columns to the way you want them and then "Join" the two datasets using "all records of both datasets" or from the sequence one? Haven't tested it yet, but might be what you are looking for. Someone might have a SQL query or other coding solution if it's more than that.