coverage analysis

[zeenia_jagga]

I have to analyze small RNA sequence reads from illumina platform. (40bp reads,illumina1.5:quality encoding).
reference genome is annotated and i am interested in determing the coverage of my mapped reads to reference genome features.
i have mapped the reads to reference genome by TopHat and Bowtie generating .bam files
i then sorted and indexed my .bam files

now i want to study coverge of each annotated feature of the reference genome.
How shall i go about it?

[mgogol]

bedtools coverageBed?

[Heisman]

GATK DepthOfCoverage is nice.