User: SGMS

gravatar for SGMS
SGMS60
Reputation:
60
Status:
Trusted
Location:
European Union
Last seen:
2 days, 14 hours ago
Joined:
4 years, 1 month ago
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Posts by SGMS

<prev • 26 results • page 1 of 3 • next >
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Comment: C: Problem with Manhattan plot
... Thanks, I have seen it and it also helped me! ...
written 8 days ago by SGMS60
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Comment: C: Problem with Manhattan plot
... Hi lurdesdl, I was wondering whether you managed to come up with a solution to your problem above. It seems I also have a a line at different p-value thresholds e.g 10^-7, 10^-5 etc. It would be great if you could give me a hint. Thanks a lot ...
written 7 months ago by SGMS60
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Comment: C: GWAS in Plink - phenotype file format
... Thanks a lot! Exactly, it's so simple but I couldn't find a source saying that precisely. ...
written 7 months ago by SGMS60
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GWAS in Plink - phenotype file format
... Hi everyone, My question may be too simple for experienced PLINK users, yet I cannot find the simplest answers anywhere online. I was looking for a sample analysis in plink to see how a GWAS is actually run as I am a super new user. I have created .ped and .map files using: vcftools --vcf ...
gwas snps plink phenotype written 7 months ago by SGMS60 • updated 7 months ago by zx87547.5k
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Comment: C: How to integrate GTEx data for variant annotation to understand the tissue speci
... Brilliant, thanks so much! This is of such a great help! ...
written 8 months ago by SGMS60
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Comment: C: How to integrate GTEx data for variant annotation to understand the tissue speci
... Hi bioinfo89, Thank you very much for your reply. Just to make sure I got it right; I downloaded the files. The rsID look-up file has variant_id and rsID columns. So when you say "Integrated the information", you mean that you matched your rsIDs of interest with the variant_ID so you could find tha ...
written 8 months ago by SGMS60
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GTEX - how to upload more than one rsIDs to get gene expression or eQTL information
... Hi everyone, I am trying to see how my variants affect the host gene -or other eQTLs- to see the direction of effect basically. I looked on GTEx but I only found the option of using one SNP at a time or put a list of SNPs but that is with additional info I don't have. Does anyone know how to u ...
rsids snps gtex written 8 months ago by SGMS60
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Comment: C: How to integrate GTEx data for variant annotation to understand the tissue speci
... Hi bioinfo89, Did you manage to find a solution? I keep looking for the exact same things but cannot find any help. Thanks a lot! ...
written 8 months ago by SGMS60
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Comment: C: Finding out if certain SNP positions fall into certain gene regions
... Thanks, my search didn't even fall on that one. It seems I will go with Pierre's suggestion and turn the SNP position into a SNP region having basically the same start and end coordinates. And then do the overlap. ...
written 8 months ago by SGMS60
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Comment: C: Finding out if certain SNP positions fall into certain gene regions
... Thanks. If I want to do that in R though, the positions will remain the same.. ...
written 8 months ago by SGMS60

Latest awards to SGMS

Great Question 7 months ago, created a question with more than 5,000 views. For findOverlaps function in R
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Extraction of SNPs from the 1000G vcf file for a set of regions
Popular Question 3.2 years ago, created a question with more than 1,000 views. For findOverlaps function in R
Student 3.2 years ago, asked a question with at least 3 up-votes. For findOverlaps function in R

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