Question: How Do I Overlay Tracks In Genomic Viewers Such As Igv Or Igb?
2
gravatar for KCC
6.2 years ago by
KCC3.9k
Cambridge, MA
KCC3.9k wrote:

The genomics browser that I usually use is IGV. In IGV, when you load a new dataset, the default behavior is to plot that data directly below all your previous plots. I would like to change this default behavior so that my plots get placed on top of each other, that is to say overlaid.

How do I do this? It's okay if the answer is to switch to something else besides IGV. I am not married to it.

visualization • 3.4k views
ADD COMMENTlink modified 6.2 years ago by Madelaine Gogol5.0k • written 6.2 years ago by KCC3.9k
3
gravatar for Madelaine Gogol
6.2 years ago by
Madelaine Gogol5.0k
Kansas City
Madelaine Gogol5.0k wrote:

This is possible using multiWigs at UCSC genome browser, but you have to also set up a track hub and I've never actually done it. Probably possible with some of the R-package based browsers as well, or if you're interested in making a figure of a certain region, you could read the data into R and make a line plot.

ADD COMMENTlink modified 6.2 years ago • written 6.2 years ago by Madelaine Gogol5.0k
2
gravatar for Istvan Albert
6.2 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

The classic design of most viewers is that of one track corresponds to one sample. Once you start overlaying data all kinds of other issues pop up on how to display the information.

The way I approach it is to merge the data and create a custom data track that contains both datasets and generates colors based on each entry (if the format allows that). The viewer will then split the view for overlapping features but that's about it.

(now if there is a better way to do this, I would love to hear it since I have been using this workaround and it is a bit tedious)

ADD COMMENTlink written 6.2 years ago by Istvan Albert ♦♦ 80k

Thanks for your feedback. I guess there is no other way to do this other than by hand. I can certainly think of several issues with overlaying data, but it's many of the same problems one has with smaller amounts of data, and we plot those on the same graph all the time ...

ADD REPLYlink written 6.2 years ago by KCC3.9k
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