getGroupBW

[rojinsafavi]

Hello,
I have some TFBS that I want to see how the accessibility changes across the cell types (groups) in those specific locations.

I used getGroupBW with default parameter, and the bigWig visualization in IGV looks like this(for two of the groups):

I was expecting to get something similar to the plotBrowserTrack output - I was wondering if you could share the difference between the bigWig visualization and the plotBrowserTrack visualization? is there a way to extract the plotBrowserTrack bed file?

Thank you very much,

-Rojin

[rcorces]

its just a matter of scale of the y axis in igv.
igv doesnt handle y axis scaling very well. you can turn on autoscale or fix your scale to something more informative.