User: Floris Brenk

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Floris Brenk780
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Posts by Floris Brenk

<prev • 160 results • page 1 of 16 • next >
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Comment: C: Imputation of chromosome X using the Michigan imputation server
... Yes just keep males and females in the same file and use as above described `plink --bfile Input_data --set-hh-missing --recode vcf --out Result_filename`. Then make sure you use the right chromosome name I remember just using X was fine and use shapeit in combination with hrc.r1.1.2016 ...
written 3 days ago by Floris Brenk780
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Comment: C: converting rows into columns and vice versa
... Here is it first mentioned in 2009 -> https://stackoverflow.com/questions/1729824/an-efficient-way-to-transpose-a-file-in-bash ...
written 9 days ago by Floris Brenk780
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Comment: C: converting rows into columns and vice versa
... How many samples do you have for your 11 million SNPs? You tried this? awk ' { for (i=1; i<=NF; i++) { a[NR,i] = $i } } NF>p { p = NF } END { for(j=1; j<=p; j++) { str=a[1,j] for(i=2; i<=NR; i++){ str= ...
written 9 days ago by Floris Brenk780
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Merge several association signals in a region and use as a phenotype
... Dear all, I got some case/control association signals in one locus and now want to perform a bit more advanced eQTL analysis in this region. I already did a standard single variant eQTL analysis and here not much interesting came out. Now I want to merge the association signals (assuming they are s ...
gwas riskscore written 9 days ago by Floris Brenk780 • updated 3 days ago by Biostar ♦♦ 20
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Comment: C: Chromosome Y imputation, any good reference panels?
... Ok thanks for your reply! As a follow up, are you aware of any tools that can identify the haplotype group based on plink data? ...
written 7 weeks ago by Floris Brenk780
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Chromosome Y imputation, any good reference panels?
... Hi all, Is anyone aware of a good reference panel for chromosome Y imputation? I know you could use 1000G, but I am more looking for a larger and more recent reference panel. Like the https://imputationserver.sph.umich.edu/ size.. ...
imputation chry genotyping written 7 weeks ago by Floris Brenk780
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Comment: C: Imputation of chromosome X using the Michigan imputation server
... Ok thanks for your reply! Looks like it is working. BTW Do you have any ideas about chromosome Y imputation? ...
written 7 weeks ago by Floris Brenk780
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Comment: C: Cannot remove subjects from Plink files
... The only explanation I can think of is that maybe the file format e.g. the spacing is different in the keep file or that plink cannot find the file... Try to extract a few lines from your map file and make a new includesubjects.txt with some random samples based on that and try it again. ...
written 9 weeks ago by Floris Brenk780
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Comment: C: Imputation of chromosome X using the Michigan imputation server
... No not yet, but they just emailed me saying that next week they will come up with a guide/pipeline how to deal with chromosome X ...
written 9 weeks ago by Floris Brenk780
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Imputation of chromosome X using the Michigan imputation server
... Hi all, Im trying to impute some genotype data on the Michigan imputation server (https://imputationserver.sph.umich.edu/ ). For autosomes this works perfect and straightforward. However for chromosome X I ran into some trouble. Initially that Eagle v2.3 does not work on chromosome X and so you nee ...
imputation genotypes chrx written 10 weeks ago by Floris Brenk780 • updated 7 weeks ago by chariko20

Latest awards to Floris Brenk

Popular Question 4 months ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
Scholar 4 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Student 7 months ago, asked a question with at least 3 up-votes. For Reformat minimac imputated files to plink file
Voter 8 months ago, voted more than 100 times.
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Difference Between Gene Expression And Transcript Expression
Scholar 10 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Scholar 11 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
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Scholar 13 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Popular Question 14 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Appreciated 15 months ago, created a post with more than 5 votes. For A: Difference Between Gene Expression And Transcript Expression
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Popular Question 18 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 20 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 20 months ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
Popular Question 20 months ago, created a question with more than 1,000 views. For SNP in Transcription factor binding site analysis
Popular Question 21 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 22 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Scholar 2.4 years ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: 1000 Genomes Ld Calculation
Scholar 3.1 years ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
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