How to do alignment quality control?

[letusgo]

I alignment my clean reads to my reference genes using Tophat, then I want to know if it did well. so I want to get the Distribution of reads on reference genes and the sequencing saturation analysis.Finally, I need to draw two figures like below. How can I do it, is there any soft can solve my problem?
Thank you

[jialicd]

same question. but you can try R to plot .