User: curious
curious • 140
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Posts by curious
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... I will give that a shot, thank you so much. ...
written 4 days ago by
curious • 140
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... I have a tabix indexed gzipped vcf that contain about 40K samples (approx 74 GB).
I just want to isolate 6 samples from this vcf, which I have in a sample list
I run on a job on a cluster that basically :
`bcftools view -Oz -S [sample list] [input vcf] -o [output vcf]`
5 hours later it is still ...
written 4 days ago by
curious • 140
• updated
4 days ago by
Pierre Lindenbaum ♦ 124k
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... I struggled with finding the mathematical explanation behind this transformation, so hopefully this helps someone. It is explained in the second paragraph of the background of this paper:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2572624/
The way I understood it is that for illumina infinium ar ...
written 28 days ago by
curious • 140
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... Thanks for responding Kevin. I am still stuck on this, but will update with an answer when I figure this out. -Brett ...
written 5 weeks ago by
curious • 140
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... I am looking at the manifests for illumina SNP arrays like this one for HumanExome-12-v1-1:
ftp://webdata:webdata@ussd-ftp.illumina.com/Downloads/ProductFiles/HumanExome/v1-1/HumanExome-12-v1-1-B.csv
If I understand correctly:
Most SNPs have one corresponding probe at a single address that is ca ...
written 5 weeks ago by
curious • 140
• updated
5 weeks ago by
Kevin Blighe ♦ 51k
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... Thank you so much this helps a lot. ...
written 6 weeks ago by
curious • 140
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consider two families like this:
FAMILY PERSON FATHER MOTHER SEX
fam1 child1 father1 mother1 m
fam1 mother1 unknown unknown f
fam1 father1 unknown unknown m
fam2 child2 father2 mother2 m
fam2 mother2 unknown unknown ...
written 6 weeks ago by
curious • 140
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... I just went through this myself. You can use different cutoffs (Tertiles, etc). Median is one of the more common cutoffs, I think this is mostly to divide the population evenly and retain all the samples. But if you look through some example papers you will see other cutoffs used. There is no hard d ...
written 7 weeks ago by
curious • 140
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... Thanks for taking the time to respond. I was trying to figure out how genomestudio calculates MAF. My guess was that they were calculating it from the genotype frequencies I gave, but I was not sure. I think I figured this out though
Allele frequency of A (minor allele):
Freq A = MAF (Minor Freq ...
written 8 weeks ago by
curious • 140
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... I am playing around with genomestudio to do genotyping of 32 SNP arrays from human samples just to learn the technique
One of my SNPs in genome studio is such:
Name: exm-rs10503253
\# Calls: 32
SNP: [A/C]
AA Freq: .125
AB Freq .250
BB Freq: .625
Minor Freq (MAF): .250
I looked at a few SNPs ...
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For A: Hardware requirement for RNA-seq
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