Bowtie2 vs Tophat Whats the difference

Question

[Abdul Rafay Khan]

Bowtie2 VS Tophat What's the difference between them?

and why Tophat required Bowtie2 to be already installed in your system?

Answer 1

[Thibault D.]

Tophat uses Botwie (or Bowtie2) to perform alignment. Then, it looks down to the unmapped reads and tries to align them using information about splicing junctions.

[Abdul Rafay Khan]

You mean reads get mis-aligned at exon exon junctions using Botwie (or Bowtie2)?

[Devon Ryan]

Bowtie1/2 will largely not map reads that overlap exons.

[Thibault D.]

One minute late, sorry !

Answer 2

[Antonio R. Franco]

Tophat does not map reads. It relays and control bowtie to do the mapping

An initial mapping is done with the entire and unmodified reads using bowtie

Then, Tophat takes the control again allowing you to splice or break the unmapped sequences into fragments (you decide the size of them..), and then it will use bowtie again to map these new (spliced) pieces in order to fit them into different putative exons or regions. TopHat will take care of everything including statistic and what has been done and how

Answer 3

[Devon Ryan]

Tophat2 uses bowtie2 to align spliced reads, since bowtie2 by itself won't align them.