User: sonia.olaechea
sonia.olaechea • 90
- 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
... 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 ...
written 11 hours ago by
sonia.olaechea • 90
0
votes
0
answers
111
views
0
answers
... 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.olaechea • 90
0
votes
0
answers
111
views
0
answers
... Great, working! But... where can I find the list of tables from which to choose the information? ...
written 6 days ago by
sonia.olaechea • 90
0
votes
0
answers
111
views
0
answers
... 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.olaechea • 90
5
votes
0
answers
111
views
0
answers
... 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 ...
written 6 days ago by
sonia.olaechea • 90
0
votes
1
answer
57
views
1
answers
... 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.olaechea • 90
1
vote
1
answer
57
views
1
answer
... 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 ...
written 12 days ago by
sonia.olaechea • 90
• updated
7 days ago by
katuckele • 10
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.olaechea • 90
4
votes
1
answer
96
views
1
answer
... 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 ...
written 5 weeks ago by
sonia.olaechea • 90
• updated
5 weeks ago by
zx8754 ♦ 7.5k
1
vote
1
answer
108
views
1
answer
... 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 -- ...
written 6 weeks ago by
sonia.olaechea • 90
• updated
5 weeks ago by
zhuantouliuzi • 0
Latest awards to sonia.olaechea
No awards yet. Soon to come :-)
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