Combining Multiple Tracks in JBrowse2

Question

[serodyc]

I am currently working on a project involving JBrowse2, which involves multiple replicates for each of two conditions. Is there a way to combine the bigwig files for each replicate into two tracks, one for each condition, when viewing them in the browser? Thanks a lot for your help.

Answer 1

[cmdcolin]

Hi there I'm a JBrowse 2 developer. One way to "combine" the tracks is to create a "multibigwig" track (or "Multi-quantitative track", just a little more wordy)

see this image for how to create a multibigwig from files in the track selector

more docs here https://jbrowse.org/jb2/docs/user_guides/multiquantitative_track/

there is no built-in way to "average out the scores of two bigwig tracks" though. you could try something like wiggletools (https://github.com/Ensembl/WiggleTools) or converting to bedgraph and doing the operation in R (bedgraph can be read.table'd, and then some statistics could be done...especially if there are matching coordinates that could be easy, just average the score columns, but not guaranteed the coordinates will match, hence wiggletools may help)