User: mbyvcm

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mbyvcm280
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280
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Location:
USA
Last seen:
17 hours ago
Joined:
2 years, 1 month ago
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c****************@gmail.com

Posts by mbyvcm

<prev • 44 results • page 1 of 5 • next >
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Comment: C: Help with Fisher test between drug-targets
... So you are saying that a single gene is targeted by multiple drugs, some disease-specific and some disease non-specific? ...
written 17 hours ago by mbyvcm280
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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 6 months ago by mbyvcm280
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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 6 months ago by mbyvcm280
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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 6 months ago by mbyvcm280
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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 6 months ago by mbyvcm280
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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 7 months ago by mbyvcm280
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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 7 months ago by mbyvcm280
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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 7 months ago by mbyvcm280
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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 7 months ago by mbyvcm280
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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 7 months ago by mbyvcm280

Latest awards to mbyvcm

Scholar 4 months ago, created an answer that has been accepted. For C: merging plink files
Teacher 4 months 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 7 months ago, created an answer that has been accepted. For C: merging plink files
Teacher 7 months 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 7 months ago, created an answer that has been accepted. For C: merging plink files

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