Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: adegent for Tajima's D:
0
gravatar for biobudhan
4.6 years ago by
biobudhan • 20
India
biobudhan • 20 wrote:

Hello everyone,

I am trying to use adegent in R for calculating the Tajima's D. I have a DNA.bin object containing my sequences from different populations. The sequences are of varying length because of the SNP and indels in them. I get the following error when I run the tajima.test function: 

Error in as.matrix.DNAbin(x) : 
  DNA sequences in list not of the same length.

How could one deal with calculating Tajima's D for sequences of different length? 

 

 

 
adegent snp fasta tajima • 1.7k views
ADD COMMENT • link •
modified 4.6 years ago by Brice Sarver • 3.5k • written 4.6 years ago by biobudhan • 20
0
gravatar for Brice Sarver
4.6 years ago by
Brice Sarver • 3.5k
United States
Brice Sarver • 3.5k wrote:

The input requires that the sequences be aligned, i.e., all sites are homologous. Think of it this way: how will you know which site an insertion or deletion corresponds to in other sequences if they are not aligned? Additionally, if sequences are not the same length, how would you calculate the number of segregating sites or pi?
ADD COMMENT • link modified 6 months ago by RamRS ♦ 27k • written 4.6 years ago by Brice Sarver • 3.5k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2168 users visited in the last hour