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Old 01-21-2011, 11:45 PM   #1
liuxq
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Location: beijing, china

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Default bowtie used by tophat

I find that tophat uses bowtie with parameter "-v 2", which will discard many low quality reads dramatically.

Is there a method to control the bowtie parameters used by tophat?

Why tophat does not use default -n mode for bowtie reads mapping?
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Old 01-22-2011, 06:57 AM   #2
Daehwan
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Quote:
Originally Posted by liuxq View Post
I find that tophat uses bowtie with parameter "-v 2", which will discard many low quality reads dramatically.

Is there a method to control the bowtie parameters used by tophat?

Why tophat does not use default -n mode for bowtie reads mapping?
I think this is a very good point, I'll make a new option for users to choose between "n" and "v" option in the next release!!

Thanks,
Daehwan
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Old 01-22-2011, 10:32 PM   #3
peromhc
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Many of us have hoped to be able to customize how Bowtie is implemented within Tophat for a long time now.. Is there any reason for this limitation, other that time spent coding the different options into Tophat?
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Old 02-22-2011, 05:34 PM   #4
xinwu
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I have another feature request about bowtie trimming option both from 3 end and 5 end. So far, we have to trim the low quality bases manually and it take redundant space for trimmed read files.
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