Illumina Read Pair Colors after Update

[bradyf...@gmail.com]

I'm trying to update from 2.1.24 to 2.3.72. Everything has been working fine for the illumina bam files I've been reading. The only issue is the coloration for the read pairs in the new version. Previously the reads for duplication = green, deletion = red, inversion = teal/darkblue and the translocations mapped to the expected chromosome locations.

After updating and using the "Color by insert size and pair orientation" as I did before. Translocations, deletions, and inversions are fine, but duplications show as red. I think this is due to the reads being longer than IGV expects so it overrides the green. Is there any setting I can change to fix this?

Thanks

[James Robinson]

Hi,

Thanks for calling this to our attention,  I wasn’t aware that the algorithm changed.  You can adjust the insert size threshold from the Alignments preferences tab.  Select “Preferences > Alignments” tab,  and look at the bottom.  To hardcode specific size threshold uncheck “Compute”.

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/6e76e941-c14e-4a5b-a8ed-7fe7837be3a2%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Jim Robinson]

The read length is not relevant, its the insert size (space between pairs).   Also,  did you mean to say "show green"? 

I think I need to see a sample of your alignments.  Go to a region not colored as you expect,  then right click over the alignments to bring up the menu and select "Export Alignments...".    This will create a sam file you can attach and I'll have a look.

Jim

On 4/28/16 6:53 AM, bradyf...@gmail.com wrote:

So the reads are 49bp. I can't seem to get the settings correct to make the duplication reads not show green. I'm using the hardcoded thresholds, tried doing both high, both low, the middle. Any ideas?

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/63c9ac98-14ff-42cc-af02-7439c9b4bc7a%40googlegroups.com.

[bradyf...@gmail.com]

Sorry this reply took so long, got side tracked by other projects. This for example should be colored red for deletion fragments. They show correctly in the previous version, but show grey here.

[Jim Robinson]

That is such a large jump in versions that is is not really useful to compare the two.   There is no special "deletion" flag,  it is coloring based on comparing insert size to statistics for individual pairs to all pairs loaded.  If you want to see more "red" you can change the thresholds in the alignment preferences window  (View > Preferences > Alignments),  look towards the bottom of the window for options.