User: ceruleanivy

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ceruleanivy20
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Posts by ceruleanivy

<prev • 36 results • page 1 of 4 • next >
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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 6 hours ago by ceruleanivy20
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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 17 days ago by ceruleanivy20 • updated 14 days ago by geocarvalho10
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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 8 weeks ago by ceruleanivy20 • updated 8 weeks ago by genePod30
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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 9 weeks ago by ceruleanivy20
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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 9 weeks ago by ceruleanivy20
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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 9 weeks ago by ceruleanivy20 • updated 9 weeks 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 11 weeks ago by ceruleanivy20
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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 3 months ago by ceruleanivy20 • updated 12 weeks ago by willgilks170
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Comment: C: Searching for ClinVar entries based on SNP annotation
... I would prefer a more automated method (programming based) that takes advantage of the latest database entries. If /tab_delimited/archive/ are the files you are referring to then I will probably have to download and decompress/merge every .gz every time I want to update my database of clinvar entrie ...
written 9 months ago by ceruleanivy20
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Searching for ClinVar entries based on SNP annotation
... I currently have a table for every patient with all of their variants on exome sequencing. One column contains the identified dbsnp code (rs). I would like to know how can I automatically generate another column that stores the ClinVar information for every available common single nucleotide polymor ...
genome R snp written 9 months ago by ceruleanivy20 • updated 9 months ago by Newgene200

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