Entering edit mode
5.8 years ago
Saeed
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0
I'm newbie in biology. I have a lot of information about copy number variation for blood cancer and I want convert CNVs to gene? How can i do that?
What do you know of CNVs? CNVs are not comparable to genes, because CNV is a type of mutation and thereby a structural abnormality in DNA and a gene is a functional unit of DNA.
I agree with the comment above; i.e. we need to know what exactly you mean. Is what you want to say "how can I map the location of each CNV to one or more genes, provided they overlap?"
Second, I would like to ask what kind of data you have (e.g. whole genome sequencing / microarray / multiple / other)?
If you already have the CNVs called and you are confident they are correctly called, then this matters less (but is still good to keep in mind), and it is a pretty simple matter to overlapping them with gene positions.
If your question is "how can I convert raw read counts from WGS to copy number variants in specific genes" that's a lot more complicated...
Let me jump in and point you to this discussion. If you have confident CNV calls then you can use bedtools to get genes overlapping with CNV segments. Let's say I am fairly confident about the CNV calls. However, I am not sure if mere overlap of genes with CNV segments is enough to assign genes to (Amp/Del) status and visualize this through tools like maftools. Please let me know your opinion about this.