User: manjumoorthy95

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Posts by manjumoorthy95

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Comment: C: Phylogenomic tree construction
... ok I will try that way ...
written 3 months ago by manjumoorthy9510
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Comment: C: Phylogenomic tree construction
... each strain has around 4.9 mb as the genome size. ...
written 3 months ago by manjumoorthy9510
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Comment: C: Phylogenomic tree construction
... But i wanted to use the entire genome of 15 strains of bacteria. ...
written 3 months ago by manjumoorthy9510
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Phylogenomic tree construction
... I wanted to construct phylogenomic tree using the whole genome of certain bacterial strains. can anybody help me with suggestions of softwares or webservers to use? ...
phylogenomics written 3 months ago by manjumoorthy9510 • updated 3 months ago by piet1.7k
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Fishers test for cog analysis
... Can anybody explain to me why do we perform fishers test on results of COG annotation. I have performed the functional annotation of proteins for a bacteria, by using Eggnog (COG Analysis). Is it mandatory to perform p test or fishers test on the results for cog analysis? ...
fishers test p value cog written 3 months ago by manjumoorthy9510
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Comment: C: heterozygous genotype in bacterial snp calling
... Ok thank you. Let me try out that way ...
written 3 months ago by manjumoorthy9510
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heterozygous genotype in bacterial snp calling
... I did snp calling for bacterial strains using GATK HaplotypeCaller. The genotypes in the result obtained had, heterozygous variants present in it. Is this possible, since bacteria are haploid. ...
haploid snp written 3 months ago by manjumoorthy9510 • updated 3 months ago by swbarnes26.2k
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Comment: C: Heatmap.2 dendrogram generation
... Iam sorry, but again what is the metric used by `hclust()` to find distance as we pass the function from `distfun()`. Is there any default metric ? ...
written 4 months ago by manjumoorthy9510
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Heatmap.2 dendrogram generation
... I used heatmap.2 in R, to create a heatmap. I used the following command : heatmap.2(as.matrix(mat_data), density.info="none", trace="none", margins =c(12,9), col=my_palette, breaks=seq(96,100,0.5), dendrogram="both") What is the method used by the heatmap.2 for dendrogram generation? Is it `h ...
R hclust heatmap.2 written 4 months ago by manjumoorthy9510 • updated 4 months ago by RamRS23k
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Comment: C: How to interpret reference homozygous genotype in the VCF file generated by GATK
... So does that mean `0/0` is not an snp? Then why is it reported? ...
written 4 months ago by manjumoorthy9510 • updated 10 weeks ago by RamRS23k

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