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Old 04-03-2013, 02:57 AM   #3
rboettcher
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Location: Berlin

Join Date: Oct 2010
Posts: 71
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Hi Amative,

what kind of reference did you provide? Bowtie2 is not splicing aware, so it is not able to deal with reads spanning splice junctions. Therefore, it can only be used to align against the transcriptome (for RNAseq). This is why TopHat was created to align against the whole genome.

Regards
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