User: spiral01

gravatar for spiral01
spiral0170
Reputation:
70
Status:
Trusted
Location:
Last seen:
3 hours ago
Joined:
1 year, 9 months ago
Email:
v*********@hotmail.com

Posts by spiral01

<prev • 70 results • page 1 of 7 • next >
0
votes
0
answers
85
views
0
answers
ensembl Chimpanzee variants - No frequency or GT info?
... I am looking for variation data for chimpanzees. The ensembl vcf files (found here: http://www.ensembl.org/Pan_troglodytes/Info/Index) do not contain frequency information, or genotypes from which to calculate frequencies. Is there anywhere I can find this information? Frequency data is essential fo ...
snp written 9 days ago by spiral0170
0
votes
0
answers
99
views
0
answers
Calculating Tajima's D from vcf data using bed files
... I need to calculate Tajima's D for vcf data, using a bed file to indicate the windows in which I want to calculate the statistic. I tried to use vcftools like so: vcftools --gzvcf file.vcf.gz --bed file.bed --TajimaD 500 --stdout > output.txt However vcftools requires that you indicate the ...
snp written 12 days ago by spiral0170
0
votes
0
answers
82
views
0
answers
popfly drosophila database: vcf files with N alleles
... I am trying to get hold of drosophila variant information for the purpose of testing a new method on. However, I am having some issues. The main dataset I am looking at is from popfly (http://popfly.uab.cat/). However when I download the data and calculate frequencies, every variant seems to have a ...
snp written 12 days ago by spiral0170
1
vote
3
answers
256
views
3
answers
Comment: C: counting number of variants within specified windows
... I had success with all the methods here but accepted this one as I understand it best. Thank you for all the help. ...
written 17 days ago by spiral0170
0
votes
3
answers
256
views
3
answers
Comment: C: counting number of variants within specified windows
... Yes, sorry I didn't make this very clear.I want to plot window number on the x axis and div (the mean number of variants) on the y axis. ...
written 18 days ago by spiral0170
9
votes
3
answers
256
views
6 follow
3
answers
counting number of variants within specified windows
... I have two tab delimited files. Each has two columns, one for chromosome and one for variant co-ordinate. I want to identify the number of positions in file2 that are within a specified window range of the positions in file1, and then check in the next window, and the next and so forth. So if this ...
genome snp written 18 days ago by spiral0170 • updated 18 days ago by cpad01124.1k
0
votes
1
answer
125
views
1
answers
Answer: A: Creating bed files for consecutive genomic windows out from polymorphisms
... I have ended up using a simple python pandas function. `df` is the table with the polymorphism position. `window` is the size of the window to use around each polymorphism. `chromSize` is the length of the chromosome in question, used to ensure the end co-ordinates do not exceed the length. de ...
written 28 days ago by spiral0170
0
votes
1
answer
125
views
1
answer
Creating bed files for consecutive genomic windows out from polymorphisms
... I have a set of polymorphisms and their position on each chromosome in a text file. I also have vcf files of variants (1000 genomes). I want to identify the number of variants within 1kb windows of each polymorphism. To do this I think I need to create bed files for each appropriate window. So fo ...
snp written 29 days ago by spiral0170
0
votes
1
answer
153
views
1
answers
Comment: C: bedtools window - killed: 9 error
... Thank you, that's an excellent explanation. ...
written 4 weeks ago by spiral0170
0
votes
1
answer
153
views
1
answers
Comment: C: bedtools window - killed: 9 error
... Thanks, this works! Would you be able to walk me through the command? I have never used brackets as you have done before here: <( gunzip -c chr1.vcf.gz | vcf2bed --sort-tmpdir="/some/large/dir" ) > Is that saying unzip the file and pipe it to the tmpdir,, before piping it to the main bed ...
written 4 weeks ago by spiral0170

Latest awards to spiral01

Supporter 5 weeks ago, voted at least 25 times.
Scholar 7 weeks ago, created an answer that has been accepted. For A: Combining vcf files so that same loci data is combined
Popular Question 16 months ago, created a question with more than 1,000 views. For Rooting phylogenetic trees in R using Ape's root function: Trees don't seem to root.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 500 users visited in the last hour