color alignment by strand not working for me in 2.3.36 (Mac)

[Jim Hu]

Just downloaded 2.3.36 to my Mac today. Viewing a bam file, I can see red/blue coloring by strand in IGV 2.2.5, but not in the new version.  The option to only show alignment files also seems to be missing in the newer version.

Did I miss a proper setting or is this a bug?

Thanks.

[Jim Robinson]

Color alignments by read strand is in the popup menu (see attached screenshot).   I'm not sure what you are referring to WRT "show only alignment files",  could you elaborate?

Jim

Just downloaded 2.3.36 to my Mac today. Viewing a bam file, I can see red/blue coloring by strand in IGV 2.2.5, but not in the new version.  The option to only show alignment files also seems to be missing in the newer version.

Did I miss a proper setting or is this a bug?

Thanks.

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[Jim Hu]

Thanks Jim,

I found the setting. I just see black reads aligned to my genome.  I tried toggling shade by read quality and turning the coloring off and back on. We are using IGV in a class here at TAMU, and we see the same problem in Ubuntu.

Regarding the menu option, it's File > Load from file. In 2.2.5 I get this:

I don't see that pulldown in the newer version.

[Jim Robinson]

Hi, WRT strand coloring,  you did confirm you are coloring by read strand correct (as opposed to another strand option)?   If that's the case I'll need to see an example file to help you further,  the option works generally. 

The file format option you point out is not available in recent versions,  we switched to using the native Mac file dialog from the custom one.

Jim