I have a question on using Bowtie vs TopHat. I do understand that TopHat call Bowtie and if followed by cufflink and cuffdiff will give transcript differential expression etc. and most of reads will be mapped to exons across junctions. Anyone has tried using Bowtie with same reads and will there be any difference in alignemnts? Theroetically, I would consider when Bowtie is used  it will align the reads to human genome at various locations not only across junsctions and the pattern may be different from TopHat alignment.  

I ran such experiment but dont find much of difference in pattern of alignments? Before I share my project I just want to have feedback from other users about their experience of using Bowtie vs TopHat for alignments.

 

Thanks.