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.cufflinks@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
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support