User: curious

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curious140
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Posts by curious

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Comment: C: bcftools view -Oz -S [sample list] [input vcf] -o [output vcf] incredibly slow f
... I will give that a shot, thank you so much. ...
written 4 days ago by curious140
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bcftools view -Oz -S [sample list] [input vcf] -o [output vcf] incredibly slow for vcf with many samples
... 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 ...
vcf bcftools written 4 days ago by curious140 • updated 4 days ago by Pierre Lindenbaum124k
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Comment: C: theta value and R value in SNP data
... 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 curious140
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Comment: C: Question about why Illumina HumanExome SNP arrays appear to detect [A/T] and [C/
... 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 curious140
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Question about why Illumina HumanExome SNP arrays appear to detect [A/T] and [C/G] SNPs by using two different probes.
... 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 ...
array gwas snp illumina written 5 weeks ago by curious140 • updated 5 weeks ago by Kevin Blighe51k
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Comment: C: Are values from the within-family id column of a plink .fam file supposed to uni
... Thank you so much this helps a lot. ...
written 6 weeks ago by curious140
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Are values from the within-family id column of a plink .fam file supposed to unique within just the family or within the whole dataset?
... 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 ...
gwas plink written 6 weeks ago by curious140
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... 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 curious140
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Comment: C: How does genenomestudio's genotyping module calculate minor allele frequency (Mi
... 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 curious140
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How does genenomestudio's genotyping module calculate minor allele frequency (Minor Freq)?
... 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 ...
maf gwas snp genomestudio written 8 weeks ago by curious140 • updated 6 weeks ago by Biostar ♦♦ 20

Latest awards to curious

Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Bioinformatics Workstation Suggestions
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Hardware requirement for RNA-seq

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