User: sonia.olaechea

Reputation:
90
Status:
Trusted
Location:
Last seen:
6 hours ago
Joined:
8 months, 2 weeks ago
Email:
s*************@gmail.com

Posts by sonia.olaechea

<prev • 34 results • page 1 of 4 • next >
0
votes
0
answers
43
views
0
answers
Manhattan plot with Bayes factor
... Hi everyone, I'm trying to do a Manhattan plot with my GWAS SNPs for which I've calculated Bayes factor. I've seen that people usually transform p-values with `-log10()`, but I would like to keep my Bayes factors untransformed. My problem is that I have values ranging from almost `0` to `10e^23` a ...
cmplot R qqman written 11 hours ago by sonia.olaechea90
0
votes
0
answers
111
views
0
answers
Comment: C: extract genes and functions +/-50kb around a SNP
... I'd like to find the names of the genes that are 50kb up- and downstream of my list of `rs` and also their functions, pathways in which they are involved and their disease associations. ...
written 5 days ago by sonia.olaechea90
0
votes
0
answers
111
views
0
answers
Comment: C: extract genes and functions +/-50kb around a SNP
... Great, working! But... where can I find the list of tables from which to choose the information? ...
written 6 days ago by sonia.olaechea90
0
votes
0
answers
111
views
0
answers
Comment: C: extract genes and functions +/-50kb around a SNP
... Hi Pierre, I'm trying to use the mysql solution you proposed in your other post, but mysql gives me the following error: `ERROR 1146 (42S02) at line 2: Table 'hg19.snp130' doesn't exist`. Is this because I'm looking at a deprecated table? Is there maybe a more updated one for snp information? Thanks ...
written 6 days ago by sonia.olaechea90
5
votes
0
answers
111
views
0
answers
extract genes and functions +/-50kb around a SNP
... Hi everyone, I have a list of SNPs (`rs`) and I would like to extract all the genes and their functions that are located 50kb up- and downstream of them. I've been trying to generate the links to the corresponding pages of `UCSC` with Excel (which is more or less automatized). But I would like to ...
gwas snp written 6 days ago by sonia.olaechea90
0
votes
1
answer
57
views
1
answers
Comment: C: bayenv2: "initial epsilon zero or 1 locus 6912"
... Hi Katie, thank you very much for your answer! I asked the developpers of the bayenv2 and they told me that the problem was that the file contained SNPs with fixed allele frequencies (the same allele in all individuals, either 0 or 1). So I filtered my data by MAF 1% and the problems was solved. I ...
written 6 days ago by sonia.olaechea90
1
vote
1
answer
57
views
1
answer
bayenv2: "initial epsilon zero or 1 locus 6912"
... Hi everyone, currently I'm running bayenv2 on my data. First,I've converted my `vcf`file into `bayenv`format but then, when I try to generate the covariance matrix, I get the message `initial epsilon zero or 1 locus 6912`. I've read that the epsilon value in `bayenv2`is related to the allele freq ...
snps bayenv2 written 12 days ago by sonia.olaechea90 • updated 7 days ago by katuckele10
0
votes
1
answer
96
views
1
answers
Comment: C: heatmap with plink genome file
... Woooow, thank you very much, it's working! Just for me to understand... what is the difference between long and wide format?? I hadn't heard before about this before. ...
written 5 weeks ago by sonia.olaechea90
4
votes
1
answer
96
views
1
answer
heatmap with plink genome file
... Hi all! I'm trying to do a heatmap with `plink`'s output for IBD calculation (`.genome`file). This file has several columns, but only three are important to me, so my parsed input format looks like this: IID1 IID2 PI_HAT ID1 ID2 0.0163 ID1 ID3 0 ID1 ID4 0.01 ...
R plink ibd written 5 weeks ago by sonia.olaechea90 • updated 5 weeks ago by zx87547.5k
1
vote
1
answer
108
views
1
answer
selscan not outputting ihs
... Hi all, I'm trying to calculate iHS with `selscan`: the program seems to apparently run normal, but my output file is empty. I've phased my data with `SHAPEIT` and tried the following commands: selscan --ihs --vcf input.phased.vcf --map input.phased.map --out output.phased selscan --ihs -- ...
haplotypes vcf selscan written 6 weeks ago by sonia.olaechea90 • updated 5 weeks ago by zhuantouliuzi0

Latest awards to sonia.olaechea

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1396 users visited in the last hour