changing the scale of the y axis

[Eric Foss]

I have used IGV to look at bam files, and IGF has always scaled the y axis to accommodate the highest read depth in the region. I recently made a .tdf file from a .bedgraph file and when I looked at it in IGV, it was scaled such that most of the data were maxed out (see attached screen shot). How can I change the scale of the y axis?

Thanks. 

Eric

[Jim Robinson]

You can right-click and select "Set data range" to manually set a scale, or "Autoscale" to dynamically set the scale based on whats in view.  By default a tdf file will scale to the 98th percentile of all data values in the file.   This can be overriden however is a "viewLimits" value is set on a track line in the bedgraph file.

Jim

I have used IGV to look at bam files, and IGF has always scaled the y axis to accommodate the highest read depth in the region. I recently made a .tdf file from a .bedgraph file and when I looked at it in IGV, it was scaled such that most of the data were maxed out (see attached screen shot). How can I change the scale of the y axis?

Thanks. 

Eric

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