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Old 06-28-2010, 08:22 PM   #1
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Location: University of Chicago

Join Date: Jun 2010
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Default Determining the number of bases and percent coverage in an aligned sequence

I have several different DNA exome and RNA sequences from the Illumina GA2 platform. For verification purposes and quality control I'd like to know how many bases the aligned sequences cover (I've already got aligned SAM files produced by Bowtie for DNA and TopHat for RNA). From the base counts I'd then like to be able to figure out the sequences' % coverage of the entire genome. Does anyone have any advice on how to go about doing this in the most efficient way possible?

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