Question: Ancient genome realignment?
0
gravatar for ermela.paparisto
8 weeks ago by
ermela.paparisto0 wrote:

I'm a little new to bioinformatics and am not sure if what I'm thinking makes sense. I am looking for a particular SNP in a gene on chromosome 4 that I believe may influence resistance to disease. I want to know if this was inherited from ancient hominins and looked it up at the ancient genome browser from the Max Plank institute. I didn't find the SNP there but the genome assembly they have is GRCh37 and my SNP is annotated in GRCh38 (rs111670008). Is it worth it to realign their raw data to the GRCh38 genome? I know this will be computer and time intensive so dont want to embark on it if I will get more or less the same answer. Thank you for any suggestions.

snp alignment assembly • 115 views
ADD COMMENTlink modified 8 weeks ago by Ventrilocus80 • written 8 weeks ago by ermela.paparisto0
1
gravatar for Ventrilocus
8 weeks ago by
Ventrilocus80
Netherlands, Rotterdam, ErasmusMC
Ventrilocus80 wrote:

If you go to dbSNP (https://www.ncbi.nlm.nih.gov/snp/rs111670008), you may find the annotation of your SNP in both GRCh37/GRCh38. In your case:

  • GRCh37.p13 chr 4 NC_000004.11:g.89300101A>G (= chr4:89300101)
  • GRCh38.p12 chr 4 NC_000004.12:g.88378949A>G (= chr4:88378949)

So, just check position chr4:89300101 in the ancient genome browser et voila!

Best,

Ventrilocus.

ADD COMMENTlink written 8 weeks ago by Ventrilocus80

Thank you! Thats very helpful!

ADD REPLYlink written 7 weeks ago by ermela.paparisto0
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