User: manjumoorthy95

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Posts by manjumoorthy95

<prev • 39 results • page 1 of 4 • next >
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paired end data with varying read length
... I have a paired end data with forward read length of 28bp and reverse read of 120bp. Is this some sequencing error? Will this cause error while mapping the paired data to a reference Genome using tools like bwa or bowtie2? ...
illumina insert size rna-seq written 7 months ago by manjumoorthy9520 • updated 6 months ago by Biostar ♦♦ 20
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dispersionPlot in cummeRbund package
... In the cummeRbund Package for analysis of CuffDiff data, the `dispersionPlot()` function allows us to know whether over-dispersion has happened with our sample. In the X-axis of the plot is the mean of the count from each samples and on Y-axis the dispersion is shown. Can anyone help me to know whic ...
dispersionplot cummerbund dispersion rna-seq written 7 months ago by manjumoorthy9520
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Comment: C: Phylogenomic tree construction
... ok I will try that way ...
written 10 months ago by manjumoorthy9520
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Comment: C: Phylogenomic tree construction
... each strain has around 4.9 mb as the genome size. ...
written 10 months ago by manjumoorthy9520
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Comment: C: Phylogenomic tree construction
... But i wanted to use the entire genome of 15 strains of bacteria. ...
written 11 months ago by manjumoorthy9520
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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 11 months ago by manjumoorthy9520 • updated 11 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 11 months ago by manjumoorthy9520
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Comment: C: heterozygous genotype in bacterial snp calling
... Ok thank you. Let me try out that way ...
written 11 months ago by manjumoorthy9520
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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 11 months ago by manjumoorthy9520 • updated 11 months ago by swbarnes27.5k
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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 11 months ago by manjumoorthy9520

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