Question: bedgraph file format in IGV: good for observing CNV ?
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Hello,

I found here that I can use begraph format to observe CNV in IGV. Suposedly, I will be able to see overrepresentations and deletions, so I converted my (aligned reads) bam file to bedgraph and opened it on IGV.

My question is if what I am seeing is actually an overrepresentation, see image attached.

 bedgraph file opened with IGV. An overrepresentation?

ADD COMMENTlink 13 months ago Pin.Bioinf • 240
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how is it different from your previous question ? How can I tell if there is CNV for specific gene in IGV?

ADD REPLYlink 13 months ago
Pierre Lindenbaum
120k
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Because I have found bedgraph format, and i am adding an image to see if i am on the correct path

ADD REPLYlink 13 months ago
Pin.Bioinf
• 240

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