User: ceruleanivy

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ceruleanivy30
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Posts by ceruleanivy

<prev • 38 results • page 1 of 4 • next >
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Comment: C: SNP tools to infer copy number variations (CNVs)
... Thanks for the response. I have targeted ampliseq NGS data on DNA from FFPE samples on ~400 amplicons. I don't have any other genetic data on these patients. The panel was designed with respect to regions that contain many informative SNPs for inferring zygosity. ...
written 3 months ago by ceruleanivy30
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SNP tools to infer copy number variations (CNVs)
... I have tried nearly every method regarding the extrapolation of different CNVs by utilizing data from coverage and reads on NGS settings, but unfortunately end up with unreliable results (too much variance among log2s to be considered trustworthy). I would like to know what tool is best for methods ...
R next-gen sequencing written 3 months ago by ceruleanivy30 • updated 3 months ago by Vincent Laufer870
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Comment: C: Different reference and variant allele in IonTorrent variantCaller
... Thanks for your response. Although I use ionReporter for annotation, I recently decided to switch to annovar and I have to admit that I've never looked up the VCF Processing Guide on the website. From my understanding of it, I should perhaps drop the VCF columns and also consider removing some varia ...
written 3 months ago by ceruleanivy30
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Different reference and variant allele in IonTorrent variantCaller
... I am doing a targeted amplicon NGS analysis on cholangiocarcinoma FFPE samples on proton sequencer on a run with 88% ISP loading. The XLS file provided, containing all the barcodes that went into analysis with the variantCaller (v5.0.2.1) software in IonServer has two different columns for reference ...
next-gen sequence sequencing written 4 months ago by ceruleanivy30 • updated 4 months ago by geocarvalho20
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Distance matrix based on mutation rates
... I would like to calculate the phylogenetic distance between 500 patients' breast cancer subtypes and need help when it comes to the right method for producing distance matrices. My patients are equally divided between the 5 sub-types (100 each) and the number of variables represents the number of po ...
software error genome next-gen written 5 months ago by ceruleanivy30 • updated 5 months ago by Genebow60
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Comment: C: Statistical significance in phylogenies
... Thanks, do you know which function will give the me the lowest possible p value between two species ? For example in a population of 10 that will eventually lead to a 10x10 matrix of p values. ...
written 6 months ago by ceruleanivy30
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Comment: C: Statistical significance in phylogenies
... I think you got it correct, I would like to receive some sort of metric to help me quantify the relationship between two species in the context of statistical significance. ...
written 6 months ago by ceruleanivy30
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Statistical significance in phylogenies
... I have constructed a distance matrix in order to produce a phylogenetic tree for 10 species in R package 'phangorn' and I would like to know how can I calculate p-values for significantly different species based purely on phylogenetic data. I would appreciate some insight, especially by the ones who ...
genome R next-gen written 6 months ago by ceruleanivy30 • updated 6 months ago by Manvendra Singh1.9k
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VisCap 'mat.cov' not found error in R
... I am using VisCap (https://github.com/pughlab/VisCap/wiki) in order to conclude copy number variations by reading BAM files created from Ion Torrent next-generation sequencing on FFPE tumor samples. After successfully creating the required output from the GATK DepthOfCoverage tool and running VisCap ...
software error R next-gen written 6 months ago by ceruleanivy30 • updated 9 weeks ago by hns130
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Infer CNVs from SNP variant allele fractions
... I am currently working on data obtained from proton sequencing (IonTorrent) on bulk tumor micro FFPE samples, using panels for exome targeting. Although I've came across some literature on that issue I am not quite experienced so I would like to ask what are the most popular algorithms/software on i ...
R next-gen snp written 6 months ago by ceruleanivy30 • updated 6 months ago by willgilks210

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