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Old 02-26-2013, 12:23 PM   #4
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,088

Just saw this over at the TopHat site. Perhaps upgrading to latest Tophat may fix your problem.

Version 2.0.8 is a quick fix release addressing the following issues:

This version correctly handles the newest version of Bowtie2 v2.1.0.
The segment mapping slow-down introduced by some Bowtie2 parameter changes in version 2.0.7 is now corrected
There is also a new version of bowtie2 (v.2.1.0) available as well.

Last edited by GenoMax; 02-26-2013 at 12:30 PM.
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