How Do I Overlay Tracks In Genomic Viewers Such As Igv Or Igb?

Question

[KCC]

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.

Answer 1

[Madelaine Gogol]

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.

Answer 2

[Istvan Albert]

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)

[KCC]

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 ...

Answer 3

[Malcolm.Cook]

Old question, new answer...

it is now possible in IGV to overlay tracks based on having a common attribute. See "Tracks > Overlay Data Tracks".

I use it often to overlay line-graphs of replicate data. It makes the variance "pop".