Hello,

I have a question regarding analysis of 3d chromatin in R. So if there is a SAM or BAM file with aligned reads to some genome, how would the analysis go in R to create contact matrix and other for viewing where are some chromosome regions that are close, TADs and compartments?

I have read about different process and pipelines in for example Python, but haven't really found much information about it in R (and haven't done such analysis of data before).

Thank you for the answer. :)