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How can I use Bowtie options from the Tophat command line?
Typing "--bowtie -option" is not recognized...
Thank you
Gilad
Typing "--bowtie -option" is not recognized...
Thank you
Gilad
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I would like that too. But it seems currently tophat is missing lots of useful options in bowtie such as "--trim", "--best", "--tryhard" etc. What bugs me the most is that Tophat returns ALL the alignments for the same read that maps multiple regions ("multihits"). I wish they could fix this very soon! -
The good thing about doing this is that the locations of the multireads is useful information that Cufflinks can now use to estimate expression.Originally posted by yuelics View Post
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