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
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written
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michael.dunne •
1 answer
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,...)
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