User: padakanti.sridevi

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Posts by padakanti.sridevi

<prev • 11 results • page 1 of 2 • next >
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Comment: C: 1000 genomes PCA for whole genome
... Can u please let me know how to go with cleaning the multi allelic sites. I am new to Genomics ...
written 9 months ago by padakanti.sridevi0
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Comment: C: 1000 genomes PCA for whole genome
... my ForMerge.list contains .bim files and MAF prune.out files ...
written 9 months ago by padakanti.sridevi0
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Comment: C: 1000 genomes PCA for whole genome
... I am using Mac , i tried sed -i' ' 's/.bim//g' ForMerge.list and it works. Iam trying to use plink --merge-list and i get this Error message : Problem with merge-list file line :should be either 2(PED/MAP) or 3(BED/BIM/FAM) fields. ...
written 9 months ago by padakanti.sridevi0
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Comment: C: 1000 genomes PCA for whole genome
... I will try that ...thank you Kevin :) ...
written 9 months ago by padakanti.sridevi0
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Comment: C: 1000 genomes PCA for whole genome
... This part below : **cd /YourDir/ ; find /YourDir/ -name "*.bim" | grep -e "MAF" > /YourDir/ForMerge.list ; sed -i 's/.bim//g' /YourDir/ForMerge.list ;** Does it find .bim files from DupsRemoved directory ? I get a ForMerge.list with zero bytes ...
written 9 months ago by padakanti.sridevi0
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Comment: C: 1000 genomes PCA for whole genome
... 1.9 is working . Also, sed -i 's/.bim//g' /YourDir/ForMerge.list shows invalid command F. ...
written 9 months ago by padakanti.sridevi0
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Comment: C: 1000 genomes PCA for whole genome
... Thank you . It was helpful ...
written 9 months ago by padakanti.sridevi0
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Comment: C: 1000 genomes PCA for whole genome
... Thank you for sharing. I tried to run this part of the code : **plink --noweb --bfile /YourDir/1000Genomes/chr$chr.1kg.phase3.v5 --list-duplicate-vars** I get the error as :plink: "unknown option --noweb" plink: "unknown option --bcf" plink: ...
written 9 months ago by padakanti.sridevi0
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Answer: A: 1000 genomes PCA for whole genome
... Will these two files be sufficient to proceed with PCA ? ...
written 9 months ago by padakanti.sridevi0
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Comment: C: 1000 genomes PCA for whole genome
... Thank you for reply :) I used the below code to convert the file to plink vcftools --gzvcf file.gz --out myfile --plink - tped. It gives me .tfam and .tped files. Will these two files be sufficient to proceed with PCA? ...
written 9 months ago by padakanti.sridevi0

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