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Old 07-04-2011, 08:53 AM   #1
GiladZil
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Location: Stockholm

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Default Setting Bowtie options from the Tophat command line

How can I use Bowtie options from the Tophat command line?
Typing "--bowtie -option" is not recognized...

Thank you
Gilad
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Old 08-01-2011, 05:39 PM   #2
yuelics
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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!
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Old 08-02-2011, 02:42 PM   #3
pbluescript
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Quote:
Originally Posted by yuelics View Post
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.
http://cufflinks.cbcb.umd.edu/howitworks.html#hmul
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