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Old 10-12-2011, 03:11 AM   #1
Inti
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Location: Mexico city

Join Date: Jul 2008
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Default Strand orientation after tophat mapping

Hi guys,
I'm doing a strand specific RNA-seq with dUTP incorporation during the second strand synthesis of cDNA and posterior UDgase treatment. after the mapping of the reads using tophat I get the reads in an opposite orientation of the gene (see attachment). Since I'm sequencing only the first strand I suppose the I would get the tags in the same direction of the genes is that correct? so, could this inversion be cause by the mapping with tophat?
thanks for your comments!
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