Question: Batch query reference nucleotide
0
gravatar for jennagu
12 months ago by
jennagu0
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???

Thanks!

snp reference sequence genomic • 321 views
ADD COMMENTlink written 12 months ago by jennagu0
1

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
T
>hg19_ct_UserTrack_3545_1 range=chr12:103246593-103246593 5'pad=0 3'pad=0 strand=+ repeatMasking=none
G
>hg19_ct_UserTrack_3545_2 range=chr12:103246654-103246654 5'pad=0 3'pad=0 strand=+ repeatMasking=none
G
>hg19_ct_UserTrack_3545_3 range=chr12:103246681-103246681 5'pad=0 3'pad=0 strand=+ repeatMasking=none
G
ADD REPLYlink modified 12 months ago • written 12 months ago by Eric Lim1.3k
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