color the positive and negative strand

[beancoco]

Hello.I‘m using this software and it helps me a lot.
I was wondering if it could color the positive and negative strand .

Thank you.

[jrobinso]

Hi I'm not Steve but I think I can answer this one. There are 2 ways to do this, actually 3.

To color by strands temporarily use this command

preference SAM.COLOR_BY READ_STRAND

To do this permanently, or until you change it, open prefs.properties in your "igv" folder with a plain text editor. Be sure IGV is not running when you do this. Add the following line

SAM.COLOR_BY=READ_STRAND

The "igv" folder is under your home directory.

Or, open IGV, load a bam file, right click, and select "Color alignments by> read strand". Then shutdown IGV. This is another way to accomplish the above with manual editing the prefs.properties file.

[stevekm]

@jrobinso do you know where to find a list of these available preferences that can be set this way? I saw the page here;

https://software.broadinstitute.org/software/igv/prefs.properties

but it does not describe this preference SAM.COLOR_BY, or much of anything else.

If there was a list of these preferences then I could easily add an option to the script to include them in the IGV .bat file.

Thanks

[stevekm]

a bit of digging on Google lead me to an example in a repo here;

https://github.com/lbergelson/variant-to-igv/blob/master/igv.prefs.properties

and what seems to be a larger list here;

https://github.com/igvteam/igv/blob/master/src/main/resources/org/broad/igv/prefs/preferences.tab

[jrobinso]

@stevekm You found the list before I could respond. The second reference is the most complete list.

[stevekm]

I am gonna mark this as an enhancement since it shouldnt be too difficult to bundle extra preferences into the .bat file, though at the moment I do not really have an ETA for when I might implement it.