User: ISB

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ISB10
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Last seen:
11 months, 1 week ago
Joined:
4 years, 2 months ago
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i**********@medisin.uio.no

Posts by ISB

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Interpretation of control strip and beta density plots for Illumina methylation
... My understanding is that the densityplot gives us a per-sample distribution of avarage beta values- The expected distribution is bimodal with the two peaks that you have in you figure, representing unmethylated and methylated signals. I expect the density plot is of raw data? I would be a little con ...
written 11 months ago by ISB10
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Comment: C: Use egrep on only one column
... Sorry for the misunderstanding! ...
written 3.7 years ago by ISB10
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Comment: C: Use egrep on only one column
... Awesome! Thank you very much! This was exactly what I needed ...
written 3.7 years ago by ISB10
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Comment: C: Use egrep on only one column
... Thank you, but these commands leave me with only the two first columns ...
written 3.7 years ago by ISB10
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Comment: C: Use egrep on only one column
... Terrific! But, I also want to keep the first column ("6"), do you know how to adapt it for doing so? Thank you soo much! ...
written 3.7 years ago by ISB10
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Use egrep on only one column
... Hi, I have a table like this; 6 6:29002062:rs7755402 0 29002062 G A 6 6:29004091:rs9468471 0 29004091 A G 6 6:29006250:rs9468473 0 29006250 A G 6 6:29006493:rs9461499 0 29006493 ...
grep unix written 3.7 years ago by ISB10 • updated 3.7 years ago by Rohit1.4k
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convert SNP annotation to rsIDs
... Hi, I have pink files with SNPs annotated like "exm" or with chromosomal position followed by the rs ID, > 6:33960611:rs2495990 0 33960611 A G > 6:33962404:rs2130410 0 33962404 A C Does anyone know how I can change the bim fil ...
plink snp bim written 3.7 years ago by ISB10
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Trouble after imputation with minimac
... Hi all, I have followed Minimac cookbook, http://genome.sph.umich.edu/wiki/Minimac:_1000_Genomes_Imputation_Cookbook#Questions_and_Comments to impute with 1000 genome V3 as reference. However, the output files show alleles as R`s, I`s and D`s in stead of A,T,C,G for some of the SNPs. Have anyone e ...
imputation minimac genetics snp written 4.2 years ago by ISB10 • updated 4.2 years ago by venks710
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Answer: A: Reformat minimac imputated files to plink file
... Use fcgene to convert minimac output to PED/MAP files. You can also use rsq as filter: fcgene --minimac-prob minimac_output.prob --minimac-infominimac_output.info --oformat plink --rsq 0.3 --out plink_files ...
written 4.2 years ago by ISB10 • updated 10 months ago by _r_am30k

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Popular Question 3.1 years ago, created a question with more than 1,000 views. For Trouble after imputation with minimac
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Use egrep on only one column

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