I am attempting to identify convergent and divergent transcription (bidirectional promoters) in several thousand genes that contain a protein TF I am interested in. I have read a paper that uses a sequencing technique known as NET-Seq to do exactly this, however I don't have access to NET-Seq data.
What I do have access to is Pol II CHIP data, and GRO-Seq data. Essentially I would like to re-create the heatmaps and metagenes seen in Figure 3A for my dataset.
I am wondering if it's possible to identify regions where convergent and divergent transcription are taking place using GRO-seq data, obtain a list of coordinates for convergent transcripts and divergent transcripts and then overlap chip-seq data at these regions to produce something similar. Is there a package in R, or a tool that can be used to do this? Or would this have to be a custom made solution? And if so, how would you approach identifying these sites?
For context, I am trying to identify which genes show bidirectional transcription, versus uni-directional transcription.
Any help is greatly appreciated.