Entering edit mode
6.0 years ago
jennagu
•
0
Hi. I have a long list of genomic locations and I would like to batch query for the corresponding reference nucleotide.
For example, here is a list of four hg19 genomic locations:
- chr12:103246681
- chr12:103246654
- chr12:103246593
- chr12:103237454
I want the reference nucleotide for each location. The answer is actually G for all four of them. I know how to get this answer by searching one at a time in the UCSC browser, but I need a way to search for hundreds at a time.
Any ideas???
Thanks!
If you have programming experience, there are many ways to do it. If you don't, have you tried UCSC Table Browser? Import your coordinates as a custom track in 'chr start end' format and you can get sequences from a list of coordinates very easily. Because UCSC uses 0-based coordinate, chr12:103246681 should be entered as 'chr12 103246680 103246681'.
One of your coordinates returns a T.