track height not changeable/resets automatically

[Malte Morische]

Dear developer team,

I have an issue with IGV (2.4.10):
I tried comparing 3 mutant tracks to 3 wild type tracks on the program, the tracks where to high for displaying them all one one screen, so I changed the track height to a value that all can be displayed fully on screen at the same time.
It worked out well until I passed 25 kB on Chromosome 1, however the track height automatically resets itself to 541 (amount shown when selecting all 6, right click>change track height); changing that value does unfortunately not change anything, when looking at it once more after its 541 again.
Changing it over main menu>tracks>set track height does not make any difference.

I tried a few things to work around it:

- skipping to Chromosome 2, but the problem occurred from the very beginning there
- taking only1/2 tracks of wild type/mutant each
- tried using different data set (another 3 wild type and 3 mutant), also tried only using 1/2 tracks each here, unfortunately didn't change anything


I don't know what else to do in this case and I hope you can give an answer. Sorry I can't provide more information, I'm very new to the program (just started yesterday). I also asked other people in my lab who work for a longer time with the program what to do but they didn't know an answer and they said the track height when opening the files in the program was unusually high.

Please excuse my English since it's not my native language.

Thank you in advance,

Malte

[James Robinson]

We need to know what type of tracks.   BAM file (alignments0?  Variants (VCF)?   Bed file?   Something else?

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/29ec7c53-5565-4fa0-aa48-3e234dc316c8%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Malte Morische]

Thank you for your fast answer. All 6 files are .BAM type and they are in a folder with the matching .BAM.BAI files

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BpsjQaCvTS1jjgXAkMm1zUiCQAoRD04qFAL80%2B3H4OFCzA%40mail.gmail.com.

[James Robinson]

This doesn't make a lot of sense to me if they are BAM files,  perhaps if you made a screenshot it would help.   By default each BAM file is displayed in a separate panel with a scrollbar.   The track height of a BAM file is the height within that panel, it will not have any effect on the height or screen area of the other BAM files, which are in other panels.

To get more control of the track heights for your situation you can select  "View > Preferences > General tab" and select "Display all tracks in a single panel" as shown in the screenshot.   Then quit IGV and restart and load your BAM files.   

Additionally, you might want to not show the coverage track with that many BAM files.   To set this up by default select "View > Preferences > Alignments"   and un-check Coverage Track in Track Display Options.   This will give you more room for the alignments.  

It is difficult to see 6 experiments at the level of alignment data in one screen,  Variants  (VCF) files are usually more appropriate for this type of comparison.   

​
​

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAEh3ycykYEyYYcwmX42crZVch4KnrrdyuKrtSz5FhHyeGL7XMQ%40mail.gmail.com.

[Malte Morische]

It changes from one view to the other and jumps between them randomly while scrolling; there also are some intermediates (last picture(3)). "Display all tracks in one panel" was already ticked; not showing the coverage track unfortunately did not change anything. the view  one the second picture (smaller tracks) is the one desired, made it look that way by choosing "tracks>fit data" to window in the main menu. I will ask my coworker if there are any vcf files available as soon as she comes in tomorrow or is there a way to do that one your own, maybe directly in the program?

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2Bpvgr96W7%3DKt3ja0%3DwzNu6RR0PFbC%3DxvSnOsNGycRXua%3Dw%40mail.gmail.com.

[James Robinson]

Ahh, ok, I see what's happening here.  Sorry for the suggestion to put them in one panel,  that was wrong.   They are auto-sizing as you move around to fit all the alignments in the window.   That is how it works, there is nothing you can do about that currently.   If you uncheck the "single panel" option you will get a scrollable panel for each BAM file.   There is no easy way to set the height of each panel,  you must use the divider bars between them.   However, the panels themselves will not change size as you move around.   The panels have scrollbars so they don't need to change size to control for coverage depth.     

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAEh3ycxgcybtdo3XL4jaFOr8XZi9LyGFXO7qX1cTRjtdM11kNg%40mail.gmail.com.

[James Robinson]

And I should point out an important distinction for this context.   Panels contain tracks.   Panels are not tracks,  and setting "track height" will have no effect on the height of the panel containing it.   So, again, in the default case, a panel will be created for each BAM file, and there will be 2 tracks in the panel (coverage and alignments).    If you are not interested in the coverage data you can turn that off, as you discovered.

[Malte Morische]

ah okay I did not really get that til now, thanks for pointing that out. Is there a way to change the panel height permanently?

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BptH8eSCfYhX1uWkiiAFPukNPTLPR%3DMGC17Y3kQmdUyCGg%40mail.gmail.com.

[Malte Morische]

good that you pointed that out, was not really clear to me til now.I will try to look at the data in that way then; it was a good suggestion to turn coverage tracks off, it makes it all a little easier.

thank you very much for your help, have a nice day

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BptH8eSCfYhX1uWkiiAFPukNPTLPR%3DMGC17Y3kQmdUyCGg%40mail.gmail.com.