Inconsistent Track Order in IGV Sashimi Plot

[xiaol...@gmail.com]

Hi, All,

I am using IGV 2.19.5 on MacOS (Apple Silicon). It happens to me very often that the order of alignment tracks in Sashimi plot is not consistent with the order of these tracks in the main panel (screenshot attached). Is there a way to re-order alignment tracks in Sashimi plots?

Thanks,

Xiao

[igv-help]

Hi Xiao,

In the screenshot you show the placement of the coverage tracks, but it's the alignment tracks that are used for the Sashimi plot and it's their order that determines the order in the plot. I can't tell if the alignment tracks are just scrolled off view or if you have selected to hide them. If they are hidden, try unhiding them and rearranging them in the desired order and then you can hide them again.

Helga

[X L]

Hi Helga,

Thank you for your suggestions! I unhid the alignment tracks and reordered them, which resolved the issue. The alignment tracks are quite large, so it required a lot of scrolling to organize them, but it works now. I was wondering why the coverage tracks and alignment tracks for the same BAM files are not displayed together by default?

Best,
Xiao

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[igv-help]

Hi Xiao,

Glad to hear that worked for you. By default the coverage and alignment tracks are displayed together when you load them into IGV. However, for flexibility in the display, you can move them separately after they have been loaded. If you move only the coverage track, the alignment track is not automatically moved along with it.

Helga

[X L]

Hi, Helga,

I see. Thank you very much! My alignment tracks are usually hidden. Now I know I need to show them first, and then move them to order.

Best,

Xiao

To view this discussion visit https://groups.google.com/d/msgid/igv-help/7fada448-0520-46f7-a36a-bd1d8224db3an%40googlegroups.com.