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Old 10-28-2009, 01:41 PM   #1
Cole Trapnell
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Location: Boston, MA

Join Date: Nov 2008
Posts: 212
Default TopHat 1.0.12 release

Hi all,

I just wanted to let you know that I've posted a fix release of TopHat that addresses a fairly serious recently introduced bug. If you are using short (~36bp) reads with TopHat 1.0.11, I strongly encourage you to upgrade. The bug drastically reduced sensitivity for some data sets.

Thanks for your patience.

Cole Trapnell is offline   Reply With Quote
Old 10-29-2009, 12:09 PM   #2
Location: North Carolina

Join Date: Nov 2008
Posts: 21
Default tophat unmapped reads


I was planning to extract the unmapped short reads when running tophat, where are those unmapped reads stored? is there any easy way to do this?
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