Question: Bowtie Vs Tophat
0
vasu punj • 360 wrote:
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.