User: mbyvcm

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mbyvcm260
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USA
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14 hours ago
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1 year, 7 months ago
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Posts by mbyvcm

<prev • 43 results • page 1 of 5 • next >
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Comment: C: plink epistasis result
... you used *--epi1 0.05*. What happens with *--epi1 1*? If you use 0.05 threshold, then your output file we be missing all pairwise interactions that do not report a p-value <=0.05. ...
written 18 days ago by mbyvcm260
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Comment: C: plink epistasis result
... If you post your log here that would help. It could be because, by default, PLINK will only output SNP x SNP interactions which pass a given p-value threshold, which is controlled with the *--epi1* flag. Does setting '--epi1 1' work? ...
written 18 days ago by mbyvcm260
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Answer: A: Replace vcf in-house variant IDs with dnSNP variant IDs
... I have done very similar annotation tasks using the [BCFtools annotate][1] function [1]: https://samtools.github.io/bcftools/bcftools.html ...
written 19 days ago by mbyvcm260
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Comment: C: Require help in using PLINK flags and scripts
... can you post the first few lines from you bed file ...
written 26 days ago by mbyvcm260
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Answer: A: PLINK- chromosome ID disappears after running association tests
... The first column is CHR and the second is SNPID. Have you got these the wrong way around? I think that chromosome has to be numeric and, because yours is not ["supercont1.1004_pilon"], it is returning a null ('0') chromosome value. You are probably also correct that only a chromosome value between ...
written 4 weeks ago by mbyvcm260
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Answer: A: Is there a quick method to extract regularly-spaced features/SNPs from a VCF fil
... I'm not sure I fully understand why you want to arbitrarily select SNPs at a given distance. But I think you may be looking for the "--thin" flag in [VCFtools][1]. Also take a look at [this][2]. I have never used it, but I hope it helps. [1]: http://vcftools.sourceforge.net/ [2]: https://sourc ...
written 4 weeks ago by mbyvcm260
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Comment: C: finding the gene contain the snps ID
... If you follow the link and look at the PDF documents ('GenomicRanges HOWTOs') halfway down the page, all will be revealed! This does require some knowledge of R, but a little time spent now is, in my honest opinion, well worth it. ...
written 4 weeks ago by mbyvcm260
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Answer: A: finding the gene contain the snps ID
... For these types of genome annotation tasks [GRanges][1] is great. [1]: https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html ...
written 4 weeks ago by mbyvcm260
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Comment: C: Help with NGS analysis
... Sounds like you could do with a collaborator. Where are you based? I'm sure there must be others at your institute that have experience with NGS. ...
written 4 weeks ago by mbyvcm260
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Answer: C: merging plink files
... The MAP line generated in the error looks like a PED line. Either your files (.map .ped) are named incorrectly, or you need to change the order you read them into PLINK. Your FID and IID should be alphanumeric. Removing the '-' may help? ...
written 4 weeks ago by mbyvcm260

Latest awards to mbyvcm

Scholar 4 weeks ago, created an answer that has been accepted. For C: merging plink files
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Is there a quick method to extract regularly-spaced features/SNPs from a VCF fil
Scholar 4 weeks ago, created an answer that has been accepted. For C: merging plink files

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