How to overlay tracks in IGV?

Question

[cthangav]

I am trying to overlay these four tracks on IGV so that they are color-coded by importance, however the overlay tracks feature isn't working. When I select Tracks > Overlay Data tracks, a dialogue box pops up saying "overlay tracks by" and the only option is "none". How do I overlap the tracks? Is this feature only for bigwig files? I'm using simple bed files. If this is not possible to do with bed files, is there any other software that can overlap tracks like this?

[Ram]

Could you maybe operate on the BED files and add a column to color by in the final BED product?

[cthangav]

Is there an option for that in IGV where you can color by a particular column? Or something in R?

[Ram]

Is there an option for that in IGV where you can color by a particular column?

My gut tells me there should be. The only way to know for sure is to try.

[cthangav]

My gut tells me there should be too, but it seems IGV isn't very bed file friendly haha

[Ram]

I guess not - there seems to be a way to color an entire BED but not color subsets of it differently.

Answer 1

[Malcolm.Cook]

No - you can not use IGV's "Tracks > Overlay Data Tracks" feature with tracks from .bed files because IGV considers them "Feature Tracks" as opposed to "Data Tracks" (which includes .bigwig files) (for more on the distinction, see https://software.broadinstitute.org/software/igv/PopupMenus#DataTrack)

You could combine your four .bed files into a single .bed file, and specify each feature's color in the 9th column, named itemRbg (c.f. https://www.ensembl.org/info/website/upload/bed.html).

But what are you really trying to do? Is "overlay" the right operation? What does "importance" mean? What do your colors represent? In your example data many of the features overlap each other. Do you want to combine them somehow in the results, perhaps by only taking the most "important" feature? What if they only partially overlap? Answering these questions, and having a worked out example of how the combined track should appear, would help us help you produce it.

[cthangav]

Thank you for the response! This is what I was trying to do so I tried adding that itemRbg column- but I haven't been able to successfully change the track color using that column. Here is an example of the bed file I made but the track remains blue.

track name=working itemRgb=On
chr18   84934083    84934737    .   .   +   84934083    84934737    0,255,123
chr18   84945421    84945702    .   .   +   84945421    84945702    0,255,123
chr18   84945803    84946141    .   .   +   84945803    84946141    0,255,123
chr18   85503159    85504042    .   .   +   85503159    85504042    0,255,123
chr4    98727851    98728474    .   .   +   98727851    98728474    0,255,123
chr2    146299896   146300538   .   .   +   146299896   146300538   0,255,123
chr2    146218142   146218749   .   .   +   146218142   146218749   0,255,123

To answer your question, Yes they're overlapping because they're actually all the same (single) bed file, just including less or more of the regions. These are enhancers that have been ranked by regulatory strength using a software called PECA (https://github.com/SUwonglab/PECA) which generates a list of the most active enhancers. the 200 file is the top 200 in the list, the 1000 the top 1000, and so on. However the option you suggest to color code them all on the same track is much more preferable.

[cthangav]

Oh I see that once I zoom into a chromosome, it changes the color. but it does not change the color of the entire track (the Manhattan plot), that remains blue. Is there no way to color code the Manhattan plots? I would need the full genome, preferably binned as pictured above.