User: Mike Dacre

gravatar for Mike Dacre
Mike Dacre30
Reputation:
30
Status:
New User
Location:
Stanford, CA
Website:
http://web.stanford.ed...
Twitter:
MikeDacre
Scholar ID:
Google Scholar Page
Last seen:
3 months, 2 weeks ago
Joined:
4 years, 8 months ago
Email:
m*********@gmail.com

I work with Hunter Fraser's group at Stanford, my research is entirely computational, and I work on a variety of projects relating to understanding the evolution of gene expression and how changes in gene expression can lead to disease. I also maintain all of the computational resources for the lab, including our 160-core cluster.

Posts by Mike Dacre

<prev • 12 results • page 1 of 2 • next >
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Comment: C: Get LD data for any two SNPs
... plink1.9 offers this functionality, as answered by @chrchang523 In case anyone else wants to do this, I wrote a little package based on plink and LDlink that allows many-to-many LD lookup. Basically, provided two SNP lists, it creates a list of SNP LD pairs between each SNP in the first list and ev ...
written 3 months ago by Mike Dacre30
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Comment: C: Get LD data for any two SNPs
... Yes! It looks like that does work, I am not sure how many queries their API can tolerate, but I am going to try this tonight to see. I also want to compare this to running the calculations with plink/vcftools to see which is faster/more stable. Thanks! ...
written 4 months ago by Mike Dacre30
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Comment: C: Get LD data for any two SNPs
... Thanks! That is great, but unfortunately it doesn't include the directionality, what I really need to know is what SNP2 is given some value for SNP1 (i.e. SNP2 is T 90% of the time when SNP1 is G) ...
written 4 months ago by Mike Dacre30
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Comment: C: Get LD data for any two SNPs
... It turns out that LDLink does this beautifully for a single pair of rsids, but it doesn't seem to work in batch mode: https://analysistools.nci.nih.gov/LDlink/ ...
written 4 months ago by Mike Dacre30
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[SOLVED] Get LD data for any two SNPs
... Is there a good way to take any two SNPs and pull out the LD between them, particularly the R-squared and **the directionality of the linkage (e.g. A in SNP1 occurs with G in SNP2 95% of the time)**? Obviously I can do this manually, but I am wanting to do it for a list of several thousand SNPs, so ...
genome linkage disequilibrium written 4 months ago by Mike Dacre30
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Comment: C: Where can I lookup old merged rsIDs?
... OK, I will try that then, thanks again! ...
written 6 months ago by Mike Dacre30
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Comment: C: Where can I lookup old merged rsIDs?
... Perfect, thanks so much Pierre. I agree that the sqlite db isn't the best bet at this point, I think I will migrate it over to postgresql, is it your experience that postresql/mysql are faster/more resource efficient for very large queries? ...
written 6 months ago by Mike Dacre30
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Comment: C: Where can I lookup old merged rsIDs?
... Yeah, that would work in principle, but I would need to put a delay of at least half a second between requests to avoid making NCBI angry, which would put the run time at around half a day. Still, it is a pretty good idea if there isn't a more efficient way to do it somewhere. I was kind of hoping f ...
written 6 months ago by Mike Dacre30
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Where can I lookup old merged rsIDs?
... I have a huge dataset of SNPs that I am trying to get hg19 locations for based only on the rsID. Right now I am doing that by just downloading the latest version of dbSNP, turning it into an sqlite database, and doing a huge long running query. This works, although it takes forever, but it has the p ...
snp written 6 months ago by Mike Dacre30 • updated 6 months ago by Pierre Lindenbaum96k
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Answer: A: Getting Risk Allele from GWAS Odds Ratio?
... Based on my work over the last few days I can say that in many cases it just isn't possible to use data from published GWAS to find the risk allele, many studies just do not publish enough information by either skipping allele information altogether and just publishing p-values, or by publishing an ...
written 6 months ago by Mike Dacre30

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