How does IGV display the peaks from a bed file?

[Neberir]

Hi,

Could someone tell me how IGV displays the peaks from a bed file in zoomed out view, and finds the mean count?

In the entire genome, there are many peaks and IGV shows the peaks in a condensed version. I am wondering if IGV has a binning criteria for the peaks or it adds up the close by peaks on to each other.

Thanks!

 

[Michael Finger]

I am new to IGViewer and bioinformatics in general, but I have this same question.

[Jim Robinson]

Hi,

In general there are no "peaks" in a bed file,  it is a format for annotations like genes etc.   To display a bar chart of numeric values a "bedgraph" file can be used, or a "wig" file.   Also,   the Encode project defines file specifically for chip peak calls,  .narrowPeak and .broadPeak,  you can load either of these.

If this doesn't answer your question please restate it with more details.

Jim

I am new to IGViewer and bioinformatics in general, but I have this same question.

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