User: sbk

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sbk40
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12 months ago
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2 years, 9 months ago
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Posts by sbk

<prev • 4 results • page 1 of 1 • next >
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Answer: A: PCA using plink files
... @MAPK, I haven't used shellfish.py so couldnt comment on it. You can probably use GCTA tool to compute PCs. Using the plink files first generate GRM files and the use the GRM file to compute PCs. # compute GRM file gcta64 --bfile $bfile --autosome --maf 0.01 --make-grm-bin --out $bfile ...
written 2.4 years ago by sbk40
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Answer: A: Full-stop/period as SNP identifier in BIM file causes error in Plink v1.9 --read
... Hi @Olavur, You can probably replace the ID column with "chr:pos:ref:alt". Example: 1:4372049:T: C. You can do this to all rows also if you don't need rsID column for further analysis. This can be achieved using following awk script: awk 'BEGIN{FS=OFS="\t"}{$2=$1":"$4":"$5":"$6;print}' filename.b ...
written 2.4 years ago by sbk40
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Answer: A: Interesting bioinformatics blogs (2017 edition)
... Thanks to @stephenturner for this wonderful compilation. He has listed out all possible medium/ways to keep up to date in the field of bioinformatics. http://www.gettinggeneticsdone.com/2017/02/staying-current-in-bioinformatics-genomics-2017.html ...
written 2.5 years ago by sbk40
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Answer: A: Genomic coordinates conversion tools - can we trust them?
... Hi Ana, I have used the NCBI's remapping service (https://www.ncbi.nlm.nih.gov/genome/tools/remap) quite a few times and I have had good results each time. If you can mention the tool you used to convert then may be people can share their experience with it. ...
written 2.6 years ago by sbk40

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Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Interesting bioinformatics blogs (2017 edition)

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