How can I get a density plot to get an idea of reads mapping to different regions of the genome.
I see that only 40% of the reads maps to CDS and around 60% mapping to UTR's or some other non-coding RNA. I have generated a bam file after mapping the reads to genome. I could like to visualize this by generating a plot kind. Since I am new-bie to this, it would be helpful if someone could help me out with what tools could be used to get this estimate and how to plot them.
I see from other posts that picard tools can be used. Also wiggle format can be used to solve this problem. Is there any reccomendation or how to get this done?