Question: Tajima'D and low-density SNP data
0
gravatar for chrys.delord
2.0 years ago by
chrys.delord0 wrote:

Dear all,

I am quite new to analysis of SNP data :-) My case is a bit particular because I only have genotypes from a few number of SNPs (~130) and more importantly, I do NOT have the associated DNA sequences because genotyping was performed through mass-spectrometry (and not sequencing!)

I was wondering if I still could use information from allele frequency spectrum and, for example, compute Tajima's D on my dataset?

Thank you very much for your enlightment!

Have a good day,

Chrys

snp • 951 views
ADD COMMENTlink modified 2.0 years ago by Kevin Blighe54k • written 2.0 years ago by chrys.delord0
0
gravatar for Kevin Blighe
2.0 years ago by
Kevin Blighe54k
Kevin Blighe54k wrote:

You could first extract sequence surround your SNPs, and there are various ways of doing this. There is a previous Biostars thread: extract sequence around snp

With the sequences, you then can create a DNAbin object using as.DNAbin() (from ape package) in R and run tajima.test() (from pegas package) on this. This will calculate Tajima's D.

ADD COMMENTlink written 2.0 years ago by Kevin Blighe54k
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: 1783 users visited in the last hour