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Old 10-28-2014, 03:21 PM   #11
sdriscoll
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Location: San Diego, CA, USA

Join Date: Sep 2009
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To cut down on the possible complexity of what is going wrong, try aligning only one of the two mate files with Tophat (i.e. as a single-end alignment) and see if Tophat manages to align more data.

Also..how long are your reads and what are you aligning to?
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/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
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