cufflinks set parameters

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cufflinks set parameters

dongdong zhaoweiming
Hi,
 
It's the first time for me to use cufflinks in galaxy, two choices confused me as follows:
Bias detection and correction can significantly improve accuracy of transcript abundance estimates.
what is the Bias correction and how does it work? And for "set parameters for paired-end reads? (not recommended)" ,what would be important difference between recommended and not recommended?
Thanks a lot!
dongdong
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Re: cufflinks set parameters

Jen Hillman-Jackson
Hello,

Apologies for the delay in reply. We wanted to point you to the
documentation for the tool and the author's help email:

Doc:
http://cufflinks.cbcb.umd.edu/index.html

Email:
[hidden email]

They also have a mailing list (the link is on the right menu bar of
their web page).

Hopefully you have already found these answers or the tool authors can
offer help beyond what is documented (the tool option documentation is
what Galaxy has on the tool form),

Best,

Jen
Galaxy team


On 10/12/11 4:00 AM, dongdong zhaoweiming wrote:

> Hi,
> It's the first time for me to use cufflinks in galaxy, two choices
> confused me as follows:
> Perform Bias Correction:
> Bias detection and correction can significantly improve accuracy of
> transcript abundance estimates.
> Set Parameters for Paired-end Reads? (not recommended):
> what is the Bias correction and how does it work? And for "set
> parameters for paired-end reads? (not recommended)" ,what would be
> important difference between recommended and not recommended?
> Thanks a lot!
> dongdong
>
>
>
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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support

Jennifer Hillman-Jackson
http://galaxyproject.org