Create junctions from Bed file for IGV visualization

Question

[Buffo]

Any advice for creating junctions file from a bed-like file?

My bed file looks like this:

chr start end chr star end

I have tried to copy the format used in TopHat (junctions file). But I can't see the junctions in IGV, just the exon-exon distance is shown. I want to visualize junctions as those contained in an RNAseq bam file. Looking for advice or recommendations, these are HiC interactions and have tried HiExplorer, Homer, HiCpro, and some others, I just want to visualize the interactions.

Answer 1

[Alex Reynolds]

Maybe take a look at the WashU Epigenome Browser for rendering interaction arcs: https://eg.readthedocs.io/en/latest/tracks.html#long-range-chromatin-interaction

You'll need to reformat your data, I suspect. The documentation should explain the requirements in more detail and how to import and set up tracks.

[Buffo]

Thanks for your suggestion. Visualizing "interaction arcs" is what I need, not sure if it is possible using Epigenome Browser, I will take a look at it.

[Alex Reynolds]

This browser does have the option to render contact arcs. You just need to bring data into the browser in the correct format, however, to make this functionality available. Hope this helps.