User: beneficii

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beneficii60
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Posts by beneficii

<prev • 30 results • page 1 of 3 • next >
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VCF file that does not have genotyping data
... So, I've got a VCF file of my whole genome sequence. I've used vcftools and plink to convert it into a bed file I merge with genotype data of people I downloaded from 1000 genomes. I then attempt to run it in admixture. Unfortunately, admixture says that an individual lacks genotyping data, so I ru ...
vcf genotyping written 2.7 years ago by beneficii60
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"Error: --recode 23 cannot be used with multi-character allele names." when converting VCF to 23andme
... I'm trying to convert a VCF file to a 23andme file. I run VCFTools to convert it to TPED. But then when I run plink1.9 to convert it to 23andme, I get the following error: "Error: --recode 23 cannot be used with multi-character allele names." What should I do? ...
vcftools plink1.9 written 2.8 years ago by beneficii60 • updated 13 months ago by nuria.mauri0
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Running R for an individual; checking admixture
... First, I would like to thank everyone for the help in getting me this far. Admixture has now run successfully and produced the files genome.Q.4 and genome.F.P I'm wanting to run R for an individual (me), but it seems really opaque how I'd do that. I'm wanting to look at things like gene clusters ba ...
R admixture plink individual written 3.0 years ago by beneficii60
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Comment: C: Problem using plink file with ADMIXTURE
... Thank you much! It's running now with no errors. ...
written 3.0 years ago by beneficii60
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Comment: C: Problem using plink file with ADMIXTURE
... And should I do this on the BIM file, or the BED file? ...
written 3.0 years ago by beneficii60
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Problem using plink file with ADMIXTURE
... I had my whole genome sequenced. In plink, I put the VCF file through and it produced 3 files: plink.bed, plink.bim, and plink.fam. As recommended by Sam in another comment, I made a backup of plink.bim and ran this Linux command on the backup: "sed 's/^chrM\s/25\t/g; s/^chrX\s/23\t/g; s/^chrY\s/24\ ...
genome admixture plink linux written 3.0 years ago by beneficii60 • updated 3.0 years ago by Philipp Bayer6.6k
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Comment: C: ADMIXTURE: "Invalid chromosome code. Use integers!"
... Thanks. I had made a backup of plink.bim before modifying it, so I was able to restore it. I used your sed function to move the backup to plink.bim while doing the modification listed above. It succeeded. Unfortunately, I am still having this error: "Error: detected that all genotypes are missing f ...
written 3.0 years ago by beneficii60
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Comment: C: ADMIXTURE: "Invalid chromosome code. Use integers!"
... I see lots of commands in PLINK, but their explanation is quite a thing to wade through. I ended up opening the BIM file in an IDE and using the Replace function. But now I have a new problem. (Won't I always?) It now ends in a message that says: "Error: detected that all genotypes are missing for ...
written 3.0 years ago by beneficii60
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Comment: C: ADMIXTURE: "Invalid chromosome code. Use integers!"
... Sam seems to have the right idea: >You can change that in the plink bim file It seems chrX is 23 and chrY is 24. The only thing I'm not sure about is chrM (MT-DNA). Would that be 25? ...
written 3.0 years ago by beneficii60
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Comment: C: ADMIXTURE: "Invalid chromosome code. Use integers!"
... And chrM becomes 25, right? ...
written 3.0 years ago by beneficii60

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