Incorrect Read Colors with Orientation+Insert Size

[bradyf...@gmail.com]

Hello,

I am using IGV 2.3.90 and I am having issues showing proper read colors for Illumina paired end reads. With orientation and insert size turned on, all reads except for translocation reads show as red. My understanding is that orientation is checked first, then insert size. In this case reads are RR orientation but colored red, but when colored only by orientation they show the correct inversion color. Changing to color by orientation only isn't a solution as I want to be able to visualize deletion reads as well. Is there a setting I can look into for this?

Thanks

[James Robinson]

Hi, you are correct, that is a bug.   The insert size color is overriding the orientation color.   I'll fix it, it will be in tonights snapshot release and the "3.0 beta" release.   Also the next 2.3.9x release but that's not scheduled yet.

Jim

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[bradyf...@gmail.com]

Great, thanks a lot of following up

On Wednesday, June 21, 2017 at 3:52:47 PM UTC-4, Jim Robinson wrote:

Hi, you are correct, that is a bug.   The insert size color is overriding the orientation color.   I'll fix it, it will be in tonights snapshot release and the "3.0 beta" release.   Also the next 2.3.9x release but that's not scheduled yet.

Jim

On Wed, Jun 21, 2017 at 8:24 AM, <bradyf...@gmail.com> wrote:

Hello,

I am using IGV 2.3.90 and I am having issues showing proper read colors for Illumina paired end reads. With orientation and insert size turned on, all reads except for translocation reads show as red. My understanding is that orientation is checked first, then insert size. In this case reads are RR orientation but colored red, but when colored only by orientation they show the correct inversion color. Changing to color by orientation only isn't a solution as I want to be able to visualize deletion reads as well. Is there a setting I can look into for this?

Thanks

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