I have done some alignments using both tophat and bowtie. Presented is an alignment of some rnaseq reads to a genome. In the top frame, using tophat, I'm showing the "acccepted_hits.bam" file. From my understanding, tophat mappings should be no worse than plain bowtie mappings, as tophat just adds another layer of alignment on top of the existing reads. How can I recover the smooth alignment as shown in the bowtie version below?