Question: Batch query reference nucleotide
gravatar for jennagu
18 months ago by
jennagu0 wrote:

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???


snp reference sequence genomic • 427 views
ADD COMMENTlink written 18 months ago by jennagu0

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.

>hg19_ct_UserTrack_3545_0 range=chr12:103237454-103237454 5'pad=0 3'pad=0 strand=+ repeatMasking=none
>hg19_ct_UserTrack_3545_1 range=chr12:103246593-103246593 5'pad=0 3'pad=0 strand=+ repeatMasking=none
>hg19_ct_UserTrack_3545_2 range=chr12:103246654-103246654 5'pad=0 3'pad=0 strand=+ repeatMasking=none
>hg19_ct_UserTrack_3545_3 range=chr12:103246681-103246681 5'pad=0 3'pad=0 strand=+ repeatMasking=none
ADD REPLYlink modified 18 months ago • written 18 months ago by Eric Lim1.4k
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