Setting Bowtie options from the Tophat command line

GiladZil · 07-04-2011, 08:53 AM

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

Thank you
Gilad

yuelics · 08-01-2011, 05:39 PM

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!

pbluescript · 08-02-2011, 02:42 PM

Quote:

Originally Posted by yuelics

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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07-04-2011, 08:53 AM	#1
GiladZil Junior Member Location: Stockholm Join Date: Jun 2011 Posts: 5	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

08-01-2011, 05:39 PM	#2
yuelics Member Location: Toronto, Canada Join Date: Apr 2011 Posts: 13	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!