Questions tagged [copy-number]

The number of copies of a gene or transcript present in a genome or cell

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What are the best practices for comparing .seg copy number outputs from iChorCNA to VisCapCancer?

I have shallow whole genome sequence data that I used the tool iChorCNA to find the mean copy number segmentation per region. The tool produces a seg file and can be seen here: https://github.com/...
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Handling of sex chromosomes in male when computing CNV copy ratio

Reading from CNVkit documentation, Mathworks documentation, Bionano documentation, for CNV calling, it seems that the common practice for array is to compute the linear copy ratio by normalizing ...
gc5's user avatar
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How to use EPIC DNAm files (.idat) to infer copy number alteration

I have access to EPIC DNA methylation profiles from approximately 40 samples. I want to use these .idat files in order to predict copy number alterations within specific promoter regions of interest. ...
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How to see if a gene is the product of copy number variation?

Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals.Copy number variation is a type of ...
Spartan 117's user avatar
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Multiple files for case in GDC data portal

I am downloading a set of Copy Number Variation samples from the GDC data API. I noticed that some cases have multiple files (aliquots) for the same case (see for example this case --- here the set of ...
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