How to find covered regions from bam file

[frewise]

Platform: Hiseq 2000
Data: RNA-Seq
Alignment: TopHat
I want to get regions covered by reads from the tophat-aligned result (accepted_hits.bam).
Is there any way for doing that?

[GenoMax]

coverageBed from BEDTools would give you what you need (http://bedtools.readthedocs.org/en/l.../coverage.html).