Question: TopHat vs Bowtie output differences
gravatar for michael.dunne
3.6 years ago by
michael.dunne10 wrote:


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?


Many thanks,


bowtie rna-seq tophat • 2.3k views
ADD COMMENTlink modified 3.6 years ago by Nicolas Rosewick9.0k • written 3.6 years ago by michael.dunne10
gravatar for Nicolas Rosewick
3.6 years ago by
Belgium, Brussels
Nicolas Rosewick9.0k wrote:

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,...)

ADD COMMENTlink written 3.6 years ago by Nicolas Rosewick9.0k
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