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.
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.
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