Questions tagged [copy-number]
The number of copies of a gene or transcript present in a genome or cell
12
questions
4
votes
1
answer
32
views
How to get cytoband and gene level copy number from genome wide SNP array copy number data?
I have (human) Illumina genome wide SNP array copy number data. For each SNP genomewide, I have Log R Ratio (LRR) and B Allele Frequency (BAF).
What tool(s) can I use to get the integer copy numbers (...
- 257
1
vote
0
answers
21
views
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 ...
- 1,783
2
votes
1
answer
80
views
How to interpret the Copy Number from pseudocount depmap portal file?
This question has also been asked on Biostars
How do I convert the Copy Number (CN) file into useful information such as HOMDEL and AMP?
This is an already normalized file with pseudo count + 1. In ...
- 224
1
vote
1
answer
49
views
Definition of Copy Number Abundance
Reading from this paper:
The remaining 9 new copy-number alterations showed altered coverage patterns on whole-genome sequencing but could not be confirmed by orthogonal methods because of their ...
- 1,783
2
votes
0
answers
123
views
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/...
- 21
1
vote
0
answers
73
views
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. ...
- 21
1
vote
0
answers
45
views
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 ...
- 137
1
vote
1
answer
41
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 ...
- 1,981
-9
votes
1
answer
534
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
...
- 1,981
1
vote
1
answer
471
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 ...
- 1,981
1
vote
0
answers
275
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 ...
- 1,783
4
votes
1
answer
93
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 ...
- 1,783