User: nataliagru1

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nataliagru160
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Posts by nataliagru1

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Error while reading mlc file from CODEML into ggtree/treeio in R
... Hello, I have run into the same issue trying to read example input mlc file from the source you provided. I simply took the example mlc file from the source and saved it as "example.mlc". Here is my command `mlcfile <- system.file("Users/Documents/ACE_PAML_analysis/", "example.mlc", package="tr ...
written 2 days ago by nataliagru160
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Comment: C: Identifying Private SNPs between multi sample vcf files.
... I would like to make an updated note. "bcftools isec" works as it should. It was unable to identify private SNPs between my multi-vcf files (Genus1.vcf vs. Genus2.vcf) because I had split these files originally from a vcf file that contained all species (Genusall.vcf). I split my vcf file based on g ...
written 23 days ago by nataliagru160
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Comment: C: Preparing a .genome file for snpEff
... Can you please clarify? You link to SNPeff webpage but no documentation. I am running into the same issue. Except I am using a genome described in snpEff database. ...
written 11 weeks ago by nataliagru160
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Comment: C: Clarification for using PSI-BLAST to generate a PSSM (am I doing it right?)
... Thank you for this information. I too am running PSI Blast and also have questions regarding num of iterations, wouldn't you want to set that parameter to 0? I am under the impression that this allows PSI-BLAST to iteratively search until convergence or until no new sequences are found? If you set ...
written 4 months ago by nataliagru160
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Comment: C: Multiple Psi-Blast Iterations From Command Line Using Remote Database
... Hello, I am not sure if I am addressing your question however when you run PSI Blast from command line as such : psiblast -query /dir/queryfile.fa -db /dir/example_database -evalue 0.001 -num_iterations 0 -outfmt 0 -out /dir/exp1_outfmt0.blast -out_pssm /dir/example.pssm -save_pssm_after_last ...
written 4 months ago by nataliagru160
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Identifying Private SNPs between multi sample vcf files.
... Dear Community, Hope all is well. I am having difficulty finding the best way to quantify Private SNPs between my multi sample VCF files. For example, I have 110 samples in my VCF file that I generated via CohortCalling using GATK. I have separated the VCF by samples who are in the same genus. ...
bcftools bcftools isec vcftools vcf-compare written 5 months ago by nataliagru160
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Comment: C: ADMIXTURE and R, color meaning on barplot in studing population ancestry, K valu
... apologies I meant to add this as a comment not an answer. Can this kindly be deleted as an answer my apologies. ...
written 5 months ago by nataliagru160
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Comment: C: ADMIXTURE and R, color meaning on barplot in studing population ancestry, K valu
... Hi Zev, Thank you for your code. The function plot.admixture is unable to save as a function in the R environment after running the loop. plot.admixture<-function("/Users/grubent/Documents/Admixture/"){ Therefore when I attempt to plot the results or save the results as you describe here: ...
written 5 months ago by nataliagru160
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Comment: C: ADMIXTURE and R, color meaning on barplot in studing population ancestry, K valu
... hello you need to add a backslash to your directory like this: "~/Documents/admixture_macosx-1.23/" ...
written 5 months ago by nataliagru160
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Comment: C: Count total number of Homozygous/Heterozygous SNPs from VCF file
... https://www.realtimegenomics.com/products/rtg-tools ...
written 8 months ago by nataliagru160

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