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.
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