Hi ,

 I am having two bam file of control and treatment sample of rna-seq data. and two target file for both control and treatment sample.When I am generating a coverage density. It says "Error in coverage.density(covlist) : 
  elements of 'covlist' do not seem to be coverages for the same targets (there are different numbers of target positions for different samples)". What should I do to plot coverage density of both control and infected sample in one graph and how do I interpret normalised graph  for rna-seq data.

Thanks