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Old 05-14-2010, 03:15 PM   #1
bzhang
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Location: California

Join Date: Apr 2010
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Default RNA-Seq analysis with paired and unpaired reads

I would like to compare the expression of two samples, one contains 60 million unpaired reads and the other contains 40 million unpaired reads and 20 million paired-end reads. What software would people recommend to use to find genes/transcripts that are differentially expressed? I have used tophat/cufflinks/cuffdiff on the unpaired reads. Can I use it utilize both paired and unpaired reads?
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