Question: How To Analyse Snp Data
0
gravatar for User 4391
9.1 years ago by
User 4391100
User 4391100 wrote:

Hi,

I am working in a biocompany and I have to analyse SNP data using Perl. I have some problem understanding SNP data. Could you please show me where to find basic information on SNPs and analysis of SNP data. Thanks you so much.

snp • 5.0k views
ADD COMMENTlink modified 9.1 years ago by Sander Timmer700 • written 9.1 years ago by User 4391100
5

You'll get better answers if you improve this question by describing your problem more specifically. If the problem is "I know nothing about SNPs", a basic web search is the place to start.

ADD REPLYlink written 9.1 years ago by Neilfws48k

Hi, please work on that question by editing it, stating what you already tried, give an excerpt of your data. Otherwise the question will be voted down, which would be justified but unpleasant for all sides!

ADD REPLYlink written 9.1 years ago by Michael Dondrup47k
3
gravatar for Sander Timmer
9.1 years ago by
Sander Timmer700
United Kingdom
Sander Timmer700 wrote:

Could you give an example about what kind of questions you would like to address? Not understanding SNP data sounds almost like you might want to start reading up on it on any source like wikipedia.

A simple starting point for "studying" known features of your given SNP would just be looking in any Genome Browsers (for example in Ensembl: http://www.ensembl.org/Homo_sapiens/Variation/Summary?r=12:79911187-79912187;v=rs1553525;vdb=variation;vf=21330552 this is the standard overview page of a random human SNP, you can change to page to add more information tracks depending on your question and what you're looking for).

But to better help you it would be better to tell us what you like to address, how many SNPs you've got, why it has to be Perl and any other relevant facts.

ADD COMMENTlink modified 12 months ago by RamRS30k • written 9.1 years ago by Sander Timmer700
1

You could use things like Biomart for finding dbSNP identifiers if you want to find other known features.

What do you not understand about your data? It looks pretty much straight forward, as you got position + some info for locations in the genome. What do you want to do with this? Can you post some lines of your SNP data and then the questions you like to address?

ADD REPLYlink written 9.1 years ago by Sander Timmer700

I don't have the data like that link. I just have the data with:

Pos_start Pos_end Score genotype reference coverage .........

So I don't know how to undestand that.

ADD REPLYlink written 9.1 years ago by User 4391100

@sander Timmer: this is the firt times I use this form so I do not know to up my data (excel data). could you show me up the excel data, picture or somthing like that?

ADD REPLYlink written 9.1 years ago by User 4391100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1449 users visited in the last hour