Add Server Tracks With Batch Script and snapshot size

[vito.ca...@gmail.com]

I am trying to setup a batch script to load five additional tracks the same way a user would use  - "File -> Load From Server", but am having difficulties implementing this into a script. 

The tracks I am trying to load are : 

• SINE
  
• LINE
  
• LTR
  
• Simple
  
• Low Complexity 
  

from Annotations -> Variation and Repeats -> Repeat Masker... 

Also, I've noticed towards the bottom of the snapshots being taken the gene has been cut off.  Is there a way to extend the size of the snapshot to encompass the gene names or reorganize the tracks to have the gene track situated at the top?  This is occurring with 5 tracks where the alignments have all been compressed.  

I tried to use the 

Thanks!

Vito C. 

[Jim Robinson]

To load those tracks you will need their URLs.  The easiest way to get that is to load them through the UI,  save a session file, then open it in a text editor to grab the URLs.

re gene track,  you can ext the height of each panel in the snapshot panel with the command "maxPanelHeight",  see http://www.broadinstitute.org/igv/PortCommands.

Jim

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[vito.ca...@gmail.com]

I have been able to successfully import the tracks I had previously mentioned with your method (Thanks!).  I have been trying to use "maxPanelHeight" and still can't seem to capture the gene name/track completely within the snapshot.   Below is how I have implemented this command within the batch script and it does show more data overall, but still misses some of the gene track.  

goto chr8:10467400-10467810

sort position

collapse

maxPanelHeight 1000000

snapshot 2.png

The increase to me seems extreme, but still doesn't change anything other than I can see more reads within the alignments.  

[Jim Robinson]

Could you attach an image?  

There is a setting to put all tracks in one panel, which I think is what you probably want here.   The preference is

IGV.single.track.pane=true

So from a batch command try

preference IGV.single.track.pane true

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[vito.ca...@gmail.com]

I have added the preference line within the script and not the gene track appears at the top which is good/fine.  

It seems when I add this line and the maxPanelHeight there seems to be some oddities going on with the track names on the left along with it being difficult to encompass all the tracks still.  I will post my batch command excerpt below and attach an image of one of the snapshots to help visualize what's going on.  

...

preference IGV.single.track.pane true

...

goto chr8:10467400-10467810

sort position

collapse

maxPanelHeight 1000000

snapshot 2.png

...

[Jim Robinson]

Hi,

I see the screenshot,  but what are the oddities you refer too?  The image should not be cut off at the bottom with the height you specify,  I will see if I can replicate that.   Regardless, an image of this size is going to be hard to do anything with.

Jim

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[vito.ca...@gmail.com]

Jim,

The track names don't look like they line up appropriately to the respective tracks.  For instance, the 20253 tracks are annotated right in the middle of the 14147 alignments.  I'm just trying to get all the tracks in one image if possible to show a comparison of how they align to the genome.  

As for the cut off at the bottom I thought that was strange with the height used too. 

Thanks,

Vito C. 

[Jim Robinson]

OK,  I see the problem, this will take some investigation.  

Do you really want to see every single alignment?  You can use down-sampling to get a good representation of the alignments in less vertical space.  

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[vito.ca...@gmail.com]

No worries.  As for the alignments, not every single one, but as many as possible for each track.  I will adjust down sampling more aggressively to try and compress the image some more.  

Thanks!

Vito C. 

[Jim Robinson]

Hi Vito,

I've been trying but so far can't reproduce your issues. I assume you
are running the latest IGV, could you confirm that? Select "Help >
About" to get the version information.

Jim

[Jim Robinson]

Here is my test script, which you can also run. The resulting image is
attached.

[vito.ca...@gmail.com]

Hi Jim,

I am currently running version 2.3.65 (94).  I see the image of your resulting script, but could you post the script so I can test on my end if possible?

Thanks,

Vito C. 

[Jim Robinson]

Oh sorry, here it is.   These are public files so you should be able to run it.

preference IGV.single.track.pane true
load http://www.broadinstitute.org/igvdata/BodyMap/hg19/IlluminaHiSeq2000_BodySites/adipose_merged/accepted_hits.bam
load http://www.broadinstitute.org/igvdata/BodyMap/hg19/IlluminaHiSeq2000_BodySites/adrenal_merged/accepted_hits.bam
load http://www.broadinstitute.org/igvdata/BodyMap/hg19/IlluminaHiSeq2000_BodySites/brain_merged/accepted_hits.bam
goto slc25a3

collapse
maxPanelHeight 1000000
snapshot 2.png

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[vito.ca...@gmail.com]

Ran the same script and attached is the image I got back.  Slightly different, not sure why.