IGV Batch script Track height

[jason...@gmail.com]

Hi.

I wrote a batch script to load three bam files at a time (I'm doing trio analysis) and take snapshots of given locations.

The problem I'm having is that the track heights for of the three panels seem to be random. Sometimes one track will take up the whole screen and the other two are squished at the bottom, and sometimes all three are evenly distributed.

Usually, the first load looks good, but each subsequent load has randomly sized track heights. 

I've extensively changed the Tracks Preferences for default height before running the script (I've tried multiple different values, etc), and I've also used the MaxPanelHeight (again with multiple values) command in my script-- they both seem to do nothing.

How can I solve this so that they are all evenly sized so that I can see a maximum amount of data for all three?

I'm running IGV 2.2 and the latest version of java 7 either on my Mac or on a linux server with X11 forwarding-- same issues with both.

I tried using an earlier version of IGV for testing, 1.5, and placing a "goto All" line after "new" seemed to help a little bit, but it wasn't consistent. (also, "goto All" in IGV 2.2 does not go to the whole chromosome view anymore-- it goes to chr2). 

Can anybody help?

Thanks,

Jason

Here's an example of my script:

new

snapshotDirectory /path/to/dir

maxPanelHeight <some integer--it doesn't seem to matter what number>

load /path/to/bam1,/path/to/bam2,/path/to/bam3

goto chr19:3113483

collapse

snapshot

new

snapshotDirectory /path/to/dir

load /path/to/bam4,/path/to/bam5,/path/to/bam6

goto chr15:32928983

collapse

snapshot

new

etc........

[freeseek]

I would also like to comment on some weird outcomes I have observed.

While increasing the height (e.g. setting "maxPanelHeight 4096" does make a difference) allows to show more of some very large tracks, I still get that some tracks are often displayed much larger than they need to be (i.e. lots of wasted white space), and sometimes some tracks are displayed collapsed, even if they were expanded with the appropriate command.

What exactly is going on when a snapshot is taken and how can these parameters be fully controlled?

[Jim Robinson]

Hi,

There can be many reasons for "lots of whitespace",  for example if a gene track is shown expanded and there is a gene somewhere with lots of isoforms the height of the track will be sized to show all those isoforms,  resulting in a lot of whitespace everywhere else.    We do not currently have a command to explicitly control individual track heights,  I have just added that to the list of future features.

With respect to tracks displaying collapsed could you supply a screenshot, and also the command used to expand them?   An example file would be helpful as well.   You can post these or email them to igv-team (at) broadinstitute.org.

JIm

[freeseek]

On Wednesday, August 7, 2013 11:44:53 AM UTC-4, Jim Robinson wrote:

With respect to tracks displaying collapsed could you supply a screenshot, and also the command used to expand them?   An example file would be helpful as well.   You can post these or email them to igv-team (at) broadinstitute.org.

I have tried IGV 2.3.20, but the problem of the tracks being squished is still not solved. Do you have time to look at it?

[Helga Thorvaldsdottir]

Hi, As Jim mentioned earlier, to look at this we need some more information. Can you supply a screenshot, and also the command used to expand them?   An example file would be helpful as well.   You can post these or email them to igv-team (at) broadinstitute.org.

Helga

[sent...@gmail.com]

I ran a script similar to Jason but dont find it in snapshotDirectory. Where else should I find them ? Is there a default directory .Can you please reply ?

[James Robinson]

Does your computer have a "find" function?  There are too many platforms and OS systems to say where the default is.

On Thu, Jun 14, 2018 at 12:31 PM, <sent...@gmail.com> wrote:

I ran a script similar to Jason but dont find it in snapshotDirectory. Where else should I find them ? Is there a default directory .Can you please reply ?

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[Dream Sentisci]

Thank you .. Actually it wasn't saving files at all because I put colon in the image name ..

My mistake ... Thanks for prompt response 

Sent from my iPhone

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