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Old 03-03-2011, 01:06 AM   #4
fkrueger
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Location: Cambridge, UK

Join Date: Sep 2009
Posts: 622
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Dear Zack,

The most likely explanation would indeed be that a sizeable fraction of you library fragments are spanning a splice junction. In these cases many fragments in your library are longer than the allowed Bowtie default fragment size of 250bp (These parameters can be adjusted with
-I/--minins <int> Default: 0.
-X/--maxins <int> Default: 250)

Using TopHat or any other splice junction aware aligner should indeed fix your problems.
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