coverage depth, bedtools and RNA-Seq experiment

[PFS]

I want to estimate the % of a transcriptome covered by an RNA-Seq experiment.

I tried to use BEDTools: one file consisted of exons only coordinates (from UCSC), the other file consisted of TopHat alignments.

The results show that 70% of the transcriptome has coverage depth 0.

I was expecting a much smaller percentage, given that I started with 100,000,000 reads x 2 (PE) and the total length of the transcriptome is 17,470,227.

Am I making a big mistake here?

ps. when I say "transcriptome", I mean the collection of all exons.

[natstreet]

Can you show us the command you used to generate that value?

[PFS]

Can you show us the command you used to generate that value?

coverageBed -abam my_accepted_hits.bam -b rn4_UCSC_kg_exons.bed -hist -s -split