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Old 12-18-2012, 03:05 AM   #2
rboettcher
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Location: Berlin

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TopHat2 is designed for RNAseq and therefore splicing aware, whereas bowtie2 is designed for DNAseq and therefore cannot handle splice junctions.

Since your RNAseq is expected to come from exons only, bowtie2 maps to the exonic regions while TopHat2 considers the introns in between as spanned by split reads or read pairs. Therefore I assume your bedgraph visualizes the spanning reads by inserting these "flat" regions in between your exons.
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