User: Laura

gravatar for Laura
Laura20
Reputation:
20
Status:
New User
Location:
UFRGS, Brazil
Last seen:
2 years, 7 months ago
Joined:
4 years, 3 months ago
Email:
a*********@gmail.com

Posts by Laura

<prev • 9 results • page 1 of 1 • next >
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Problem removing individuals in PLINK
... Hi, I'm trying to remove a few individuals from a pedfile in plink.I created the txt wif FID and ID of individuals and ran the command --remove myfile --recode --out newfile However, the newfile ped file appears to be encrypted. It does not open as a flat plain text, as it should. I tried also the f ...
remove plink pedfile written 2.6 years ago by Laura20 • updated 2.6 years ago by Biostar ♦♦ 20
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Answer: A: Mach-admix: fatal error with physical map?
... Hi, I had this problem when using mach-admix for Windows. Once I tried using it for Linux, it did not happen again. ...
written 2.6 years ago by Laura20
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continuos covariates in Plink
... I'm performing a logistic regression in Plink in a gwas data. I have age, sex and race as covariates. Should I use them as dummy categories (age and race)? ...
plink logistic written 2.9 years ago by Laura20 • updated 2.9 years ago by Floris Brenk890
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Mach-admix: fatal error with physical map?
... I'm trying to impute using Mach-Admix. The ref file is 1000G P3,v5, downloaded from MACH website. I'm imputing using chromossome chunks of 5Mb and flanks of 250kb). In my sample file there are ~800 markers (from the same splitted chromosome region) and 900 individuals.  The program shows this mess ...
physical map mach-admix imputation fatal error written 4.2 years ago by Laura20
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Comment: C: How To Get Chromosome Position Given Rs Number?
... Hello Emily, I have a data file for imputation only with rs numbers and my referecence vcf file has rsnumber:Chro:position:allele1:allele2. Biomart has the H. sapiens variation in GRCh38 and my ref. file (1KG) is in GRCh37. How could I proceed? ...
written 4.2 years ago by Laura20
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Pre-phasing for imputation BEAGLE or MACH
... Hello, I'm performing pre-phasing for imputation in MACH. However, this is very time consuming. There are 950 individuals and for chromossome 4, there are ~37.000 SNPs, for example. I've read that BEAGLE is faster but less accurate depending on sample and marker size. In this case, do you think us ...
computing time mach imputation phasing beagle written 4.3 years ago by Laura20 • updated 4.3 years ago by nchuang200
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Genotype imputation or tagging?
... Hi, I want to evaluate 41 snps in my dataset. However only 19 were genotyped by the plataform (illumina). What would be the best way to predict the missing ones? Perform genotype imputation or trying to look for tag SNPS? ...
snp written 4.3 years ago by Laura20 • updated 4.2 years ago by Biostar ♦♦ 20
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Comment: C: (beginner) Where to find a good tutorial for QC in gwas data, genotype imputatio
... Unfortunately this chapter isn’t available in my university. But thanks for answering! ...
written 4.3 years ago by Laura20
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(beginner) Where to find a good tutorial for QC in gwas data, genotype imputation
... Hello, I have recently started reading and working with bioinformatics and still have little knowledge in the area (dont have programming background). I wish to evaluate some SNPs of interest in GWAS data from dbgap. I’ve downloaded some programs (plink, haploview, mach). I read and performed many ...
snp written 4.3 years ago by Laura20 • updated 4.3 years ago by alesssia530

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