TopHat vs Bowtie output differences

Question

[michael.dunne]

Hello,

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?

Image: https://postimg.org/image/4ug24a1z9/

Many thanks,

Michael

Answer 1

[Nicolas Rosewick]

As you analyze RNA-Seq data you should always use a splice-aware aligner such as Tophat (Tophat use bowtie). Bowtie alone is not splice-aware.

Be also aware that Tophat is quiet an "old" aligner in the RNA-Seq world and "better" ones exist (STAR, HiSat2,...)