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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
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Simultaneously color reads by YC and MM/ML tag #1403

Open pre-mRNA opened 11 months ago

pre-mRNA commented 11 months ago

Would this be possible? The YC tag colors the entire alignment, whereas the MM/ML tag only typically color individual bases. It would be great to be able to visualise both simultaneously.

jrobinso commented 11 months ago

I don't know, have you tried it?

pre-mRNA commented 11 months ago

Right now, the color modes are mutually exclusive, but it should be possible to show both at the same time, using YC tag as the base alignment color and MM/ML tags for individual modified bases.

I guess this is more of a feature request than an issue.

jrobinso commented 11 months ago

Could you prepare a small dataset with "YC" and "MM/ML" tags? Just a few reads. I agree you should be able to do both. I'm surprised it doesn't color alignments by "YC" by default, in which case you could select base modifications from the menu.

pre-mRNA commented 4 months ago

Hey, sorry for the delay on my end. I've uploaded a test datasets of reads annotated with YC and MM/ML tags, mapped to HG38.

The bam file is attached:

HNRNPA1.zip

For reference, here are the views I get when I color by YC tag, and later by `base modificiation (m6A). I'm using IGV 2.17.3 It would be great to be able to see both views, with the YC tag on the bottom, and the modification calls overlaid atop this information.

YC tags view MM tags view

pre-mRNA commented 3 months ago

Bumping

jrobinso commented 4 weeks ago

@lbergelson It occurs to me that we have conflated 2 things here. Color by tag applies to the alignments, color by modifications is really how to color individual bases. Coloring mismatches, and bisulfite seq options as well. Perhaps we can split these (alignment and base color) as separate options. Its not trivial to do this and maintain the same behavior by default, and importantly the same look for the many saved sessions out there.

pre-mRNA commented 4 weeks ago

Yes, it would be incredible to split the alignment color from the modifications tag. Thanks a lot.