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Old 01-28-2011, 12:59 AM   #1
dnusol
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Location: Spain

Join Date: Jul 2009
Posts: 133
Default Running Tophat for a few samples

Hi,
This may be a naive question. I am running tophat for a set of four lanes, each coming from four different samples. I run tophat using the four fastq files separated by a comma as the manual suggests, but I am getting one single output file. Does that mean that the program thinks the four files come from the same sample and merges results?

Thanks,

Dave
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