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.
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