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:
tophat.cuffli...@gmail.com

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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___________________________________________________________
The Galaxy User list should be used for the discussion of
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