Question: TopHat vs Bowtie output differences
1
gravatar for michael.dunne
2.8 years ago by
michael.dunne10 wrote:

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

bowtie rna-seq tophat • 2.0k views
ADD COMMENTlink modified 2.8 years ago by Nicolas Rosewick8.5k • written 2.8 years ago by michael.dunne10
1
gravatar for Nicolas Rosewick
2.8 years ago by
Belgium, Brussels
Nicolas Rosewick8.5k 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 2.8 years ago by Nicolas Rosewick8.5k
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