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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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 ...
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39 views

What does these terms mean?

I am working on cancer genomics failed to follow some terms even by googling What is the difference of focal genome amplifications versus convergent amplification of given region of genome for ...
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34 views

How to find essential genes by differential expression from TCGA 3rd level CNV data?

I have two types of data one have normal patients copy number variation (CNV) data and another have tumor patients CNV data. In each file there are three columns one contain patient ID, second ...
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1answer
250 views

Extracting the number SNP in each range

I have called copy number and I have 2 files (I have shared the link of my files ); One contains some ranges ...
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1answer
290 views

Getting this information for GISTIC2

Long time I am struggling how to provide GISTIC2 required input like Num_Probes and Segment_Mean I have called somatic copy ...
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139 views

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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1answer
88 views

Compute copy number from cases and controls

I have some data on Copy Number Variation (SNP chip) for a population of samples. In particular, I have a set of samples (considered as cases) which display a specific disease phenotype, and another ...