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I need to use Bedtools utilities
Why? The only reason I can think of is "because it's a homework question".
Bedtools hint is included by @Goutham below. You must do some work yourself (read the manual page or search Biostars) to put together the necessary command line.
Yes, it is a project for bioinformatics course! However at the end I used:
intersectBed -abam sorted_reads.bam -b myfile.gtf| coverageBed -counts -abam stdin -b Imyfile.gtf>FINAL
Thanks everybody for the help!