coverage depth, bedtools and RNA-Seq experiment

PFS · 03-17-2011, 07:46 PM

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 · 03-18-2011, 01:04 AM

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

PFS · 03-18-2011, 08:27 AM

Quote:

Originally Posted by natstreet

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

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03-17-2011, 07:46 PM	#1
PFS Member Location: USA Join Date: Mar 2010 Posts: 55	coverage depth, bedtools and RNA-Seq experiment 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.

03-18-2011, 01:04 AM	#2
natstreet Member Location: Sweden Join Date: Nov 2009 Posts: 83	Can you show us the command you used to generate that value?