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.