User: michael.nagle

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michael.nagle100
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Posts by michael.nagle

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
... My VCF is in VCF format, but for the purpose of this post I opened it in a spreadsheet program and took a screenshot so that it would be human-readable. This bcftools command would work if indels were called in this VCF. As you can see in the screenshot, only SNPs have been called. My question is a ...
written 15 days ago by michael.nagle100
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Comment: C: Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
... I've edited my post to include a sample of the VCF file. Thanks. ...
written 16 days ago by michael.nagle100
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Comment: C: Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
... No, I'm working with a non-model plant organism. ...
written 16 days ago by michael.nagle100
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Post-GWAS: Determining whether SNPs represent an indel, given only SNPs
... A number of SNPs appear to be associated with a trait of interest. I wish to look into all of these SNPs and get an idea of how they affect genes and whether they correspond to insertions or deletion mutations (indels). I do not have access to genome sequence data for the GWAS population, only SNP ...
gwas written 16 days ago by michael.nagle100
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GWAS: Same workflow and inputs, different servers, very different output (EMMAX)
... Using our server, I'm trying to replicate collaborators' results using the same workflow and dataset used on their server. This is the standard EMMAX workflow detailed here: https://genome.sph.umich.edu/wiki/EMMAX For some reason, results are very different. One server seems to produce nothing but ...
server gwas C cluster emmax written 10 months ago by michael.nagle100
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Comment: C: Extra header column stopping EMMAX (C), but not seen in input files
... This one-liner says the input files are tab-delimited and I also made sure by replacing all tabs with $ and by double checking the perl code used to format the tab-delimited input files. ...
written 12 months ago by michael.nagle100
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Comment: C: Extra header column stopping EMMAX (C++), but not seen in input files
... The code works. I'm trying to look at the code to figure out what the problem with input is. The files are tab-delimited text as per EMMAX instructions. ...
written 12 months ago by michael.nagle100
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Comment: C: "Unrecognized token: C" error when using emmax-kin to make kinship matrix for GW
... This solved the problem. Thank you! ...
written 12 months ago by michael.nagle100
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Extra header column stopping EMMAX (C), but not seen in input files
... I'm using a C implementation of EMMAX for GWAS and am getting an error that I can't get to the bottom of because I don't know enough about C. I hope there's a C expert who can take a quick look at this and let me know which of my input files has the problem, and what is causing the error. **Input:* ...
gwas c++ emmax genomics plink written 12 months ago by michael.nagle100
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Comment: C: "Unrecognized token: C" error when using emmax-kin to make kinship matrix for GW
... I've looked at this part of the source code alone and in the broader context, and don't understand why it would want genotypes encoded as 0, 1 or 2 (or how this is possible) when a .tped file has G/A/T/K/0 for each. Hope somebody can clarify... ...
written 13 months ago by michael.nagle100

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