Need help reading this data

Celestic · 10-12-2018, 11:47 AM

Hi I am a computer science graduate student and need help reading some data for this bioinformatics research I am helping out on. I have a few hundred text files containing the following sample information:

Geno SNP_A-8343733 NA
Geno SNP_A-8338245 1
Geno SNP_A-8338251 NA
Geno SNP_A-8338258 0
Geno SNP_A-8344803 1
Geno SNP_A-8349310 1

I want to know how to read this data and what kind of data is this? I am new to Biology and Bioinformatics in general so any help would be greatly appreciated!

Richard Finney · 10-12-2018, 12:33 PM

check out "affymetrix array snp calling" output formats and codes

SNP_A* are snp ids (which map to dbSNPS's rsIDS)

The code is probably ...
0=AA (homozygous for the reference allele)
1=AB (heterozybous)
2=BB (homozygous for the alternative allele)

but make sure.

Celestic · 10-12-2018, 01:33 PM

Okay thank you. I found out that it is affymetrix array snp calling 6.0 but not sure what I can do with this data exactly?

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10-12-2018, 11:47 AM	#1
Celestic Junior Member Location: United States Join Date: Oct 2018 Posts: 2	Need help reading this data Hi I am a computer science graduate student and need help reading some data for this bioinformatics research I am helping out on. I have a few hundred text files containing the following sample information: Geno SNP_A-8343733 NA Geno SNP_A-8338245 1 Geno SNP_A-8338251 NA Geno SNP_A-8338258 0 Geno SNP_A-8344803 1 Geno SNP_A-8349310 1 I want to know how to read this data and what kind of data is this? I am new to Biology and Bioinformatics in general so any help would be greatly appreciated!

10-12-2018, 12:33 PM	#2
Richard Finney Senior Member Location: bethesda Join Date: Feb 2009 Posts: 700	check out "affymetrix array snp calling" output formats and codes SNP_A* are snp ids (which map to dbSNPS's rsIDS) The code is probably ... 0=AA (homozygous for the reference allele) 1=AB (heterozybous) 2=BB (homozygous for the alternative allele) but make sure.

10-12-2018, 01:33 PM	#3
Celestic Junior Member Location: United States Join Date: Oct 2018 Posts: 2	Okay thank you. I found out that it is affymetrix array snp calling 6.0 but not sure what I can do with this data exactly?