I have 2 bed files contain information about RNA-seq reads of two replicates for the same cell line, as follows:
I want to study this cell line as compared two other cell lines. So, I need to represent this cell line using one (maybe combined or merged) replicate. So, can I merge the 2 bed files directly using mergebed? or I need first to rescale libraries to the same scale to remove sequencing bias?
I want to study this cell line as compared two other cell lines. So, I need to represent this cell line using one (maybe combined or merged) replicate. So, can I merge the 2 bed files directly using mergebed? or I need first to rescale libraries to the same scale to remove sequencing bias?