Multi-alignment track display on recent IGV versions

[Yvan Wenger]

Hi !

In the past (e.g. IGV_2.3.98) I was able to see several tracks stacked within one window, for example like in this screenshots from:

https://software.broadinstitute.org/software/igv/AlignmentData

The 2 alignment tracks her feature scroll bars for each track on their rights (cropped in the following screenshot)

Is there a way to obtain a similar layout using IGV_2.12.3 ? All what I can get are alignment tracks  which I cannot resize to fit my screen, e.g.

Any hint ?

Best,

Yvan

[Yvan Wenger]

Ah !

I think that after un-selecting the option View --> Preferences --> General --> Display all tracks in a single panel, IGV needed to be restarted. My issue is solved, sorry for the spam.

Best, Yvan

[Edu Calpena]

Hi,

I'm experiencing the same issue, but the "Display all tracks in a single panel" option is already deactivated. Do you have any suggestions? 

In an older version (on another laptop), I was able to scroll through the different alignment tracks, as is also possible in the web version. However, I've tried IGV versions 2.19.2 and 2.19.5, and encountered the same problem in both. If I load (for example) three WES or WGS datasets, they all appear in a single panel (as shown by Yvan in the original message). It's quite frustrating to work with it this way.

Any help would be greatly appreciated.

Thanks in advance!

Eduardo Calpena

[igv-help]

I'm not able to reproduce your issue, here is what I see with 3 bam tracks with IGV 2.19.5.   Could you try quitting IGV, then delete or rename the file "prefs.properties" in the "igv" folder located in your home directory?  

[Edu Calpena]

Thank you for your reply. I tried your suggestion, but encountered the same problem. However, I have identified the issue. When dragging and dropping the files (three CRAM files in this case), they open in a single panel (even when the single panel option is not selected; shown on the left of the attached screenshot), whereas they open as separate tracks when loaded via File > Load from File (shown on the right of the screenshot). On previous versions I used on another laptop, it didn't matter whether I used drag and drop.

For reference, I'm using a windows laptop with IGV 2.19.5 (same behaviour with 2.19.2) and working with CRAMs. In any case, opening the files via Load from File has solved my issue.

Many thanks for your excellent tool!!!

Kind regards,

Edu