Question: How can I tell if there is CNV for specific gene in IGV?
gravatar for Pin.Bioinf
19 months ago by
Pin.Bioinf270 wrote:


I am wondering if there is a way to visualize the CNV ratio for a specific gene in IGV and how can I visualize it. If not, how can I obtain the CNV ratio?

Thank you!

igv cnv • 911 views
ADD COMMENTlink modified 19 months ago by Vitis2.4k • written 19 months ago by Pin.Bioinf270
gravatar for Vitis
19 months ago by
New York
Vitis2.4k wrote:

If you are using Illumina data for CNV discovery, there usually are two things you'll be looking for: coverage changes and breakpoints. Clean and clear-cut copy number changes are easy to spot on a coverage plot with distinct breakpoints from IGV or any other genome browser that supports BAM coverage. If you don't know where to look, coverage in sliding windows could be calculated and compared to find abnormal coverage changes standing out of normal coverage fluctuation noise.

ADD COMMENTlink written 19 months ago by Vitis2.4k
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