Hi hbeale,

Did you solve this problem at the end? I came across exactly the same issue with you.

Thanks,
Zukai

I'll look into this for the next point release.

@hbeale @zukailiu Did either of you try setting the track to "Autoscale"? That works for me, although there is a refresh problem (autoscale doesn't take effect until a repaint is forced, e.g. by dragging).

I'll add a menu item to set an explicit value, that should be there in any event, but autoscale works in the meantime.

@hbeale I might need a test set to reproduce that, it works for me with all my test datasets. For example, load the attached (after unzipping as a session) and select "Autoscale" for the Liver track, then drag to force refresh.
rnaSeq.xml.zip

@jrobinso I tried the 'autoscale' on my IGV 2.12.3 and it worked!! Thank you so much!

Interesting! I get similar results with your test data as I do with my data. It looks like the data is scaled even above 50 reads within a track (or what do you call it, probably not a track, but the distinct rows within a track that appear when you set the junction track to "expanded"), but not across "tracks".

Here's before

Here's after:

After, in the top "track", the middle-ish junction representing 1495 reads is now taller than one to the left in the same horizontal line with 693 reads, but both junction arcs are smaller than the one representing 40 reads in the "track" below it.

OK, I will look into that, I had not looked at "expanded" mode. The rows are just rows, tracks in this case would be liver and heart.

Yes I see what's happening, its autoscaling each row, which of course is not what we want.

This is released in 2.15.1