SNP's and Gene?
0
1
Entering edit mode
4.4 years ago

How to translate SNPs into gene? And gene in phenotype in bovine? Is it a program I can use?

SNP gene • 1.5k views
ADD COMMENT
1
Entering edit mode

How to translate SNPs into gene?

What does this mean? This makes no sense.

ADD REPLY
0
Entering edit mode

Thank Joe! I have a list of 17 individuals, father, mother and children. Each individual has 35,000 known SNPs. How to know the genes of these SNPs?

ADD REPLY
1
Entering edit mode

Please just stop here and go back and add much more information to your question. We don't know what format your data is in, so we can't answer this in its current form.

You also asked for bovine phenotypic information, what has this to do with your human samples? Misunderstood, my mistake.

ADD REPLY
0
Entering edit mode
SNP Name    Chr Position    Sample ID   Allele1 - Forward   Allele2 - Forward   Allele1 - Top   Allele2 - Top   Allele1 - AB    Allele2 - AB    Log R Ratio B Allele Freq   GC Score    GT Score    SNP Theta   R   X   Y   X Raw   Y Raw   CNV Value   CNV Confidence  
ARS-BFGL-BAC-11044  1   12805406    00-Touro    C   C   G   G   B   B   0.0695  0.9986  0.8378  0.8149  [T/C]   0.973   0.983   0.040   0.943   1217    5143    2.0

This is the genotyping of a bovine (Bos indicus). I want to know how to read the result, can you help me?

ADD REPLY
2
Entering edit mode

PLEASE EDIT YOUR ORIGINAL QUESTION WITH THIS NEW INFORMATION.

ADD REPLY
0
Entering edit mode

What reference genome were the SNPs called against?

ADD REPLY
0
Entering edit mode

Hi Emily! Genome of Bos indicus cattle.

ADD REPLY
0
Entering edit mode

What was the accession of the genome assembly?

ADD REPLY
0
Entering edit mode

Emily! Sorry I did not understand your question?

ADD REPLY
2
Entering edit mode

Then you have a problem. If you don't know what genome these variants were called on then you have no way of interpreting them. Species name is not enough, you need an accession number, usually a short combination of letters and numbers that indicates exactly which version of the genome you were using. If you don't know that then you don't know what is at chromosome 1, position 12805406, so there is nothing you can do with that data.

Imagine that I told you to find an important quote on page 100 of Oliver Twist. Here are all the versions of Oliver Twist that I can buy from Amazon. See if you can find the quote on page 100.

ADD REPLY
0
Entering edit mode
SNP Name    Chr Position    Sample ID   Allele1 - Forward   Allele2 - Forward   Allele1 - Top   Allele2 - Top   Allele1 - AB    Allele2 - AB    Log R Ratio B Allele Freq   GC Score    GT Score    SNP Theta   R   X   Y   X Raw   Y Raw   CNV Value   CNV Confidence  
ARS-BFGL-BAC-11044  1   12805406    00-Touro    C   C   G   G   B   B   0.0695  0.9986  0.8378  0.8149  [T/C]   0.973   0.983   0.040   0.943   1217    5143    2.0 .

Emily, this is a small sample from the result of an Illumina cattle genotyping, GGP 35K. How do I have to analyze it?

ADD REPLY
2
Entering edit mode

You have already shown us what the data looks like. I am asking you a different question: what is the genome assembly?

You need to read the specs given to you by Illumina. Somewhere in there it will say what genome assembly the variant location is listed as. Once you have that, you need to convert your data into VCF and run it through a variant annotation tool, like the VEP. If the genome assembly is not one that is included already, you will need to get a FASTA file and a GTF of gene annotation to match the assembly.

Next time: find out what data you're going to get out and how you're going to interpret it BEFORE buying an expensive Illumina product.

ADD REPLY
0
Entering edit mode

Thank you, Emily! I'll try...( My name is : Kélia Margarida Barros Freire, Brazil :) kmbfreire@gmail.com )

ADD REPLY

Login before adding your answer.

Traffic: 1027 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6