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Old 07-13-2012, 01:56 PM   #3
manianslab
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Location: USA

Join Date: Jun 2012
Posts: 9
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@liueagle, it appears that since bowtie2 by default allows less stringent matching (e.g. gaps), the number of mapped reads is higher, but tophat perhaps checks them and makes sure they meet the criteria. Due to the repeated release of betas for cufflinks2, we have put on hold the tophat2-cufflinks2 pipeline and instead are using the stable release tophat1-cufflinks1.
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