Hi Irene,
You likely saw the reply, but for everyone else:
http://user.list.galaxyproject.org/cufflinks-reference-annotation-td4654251.html

Next time, posting to a single list is best. For questions like this one, galaxy-user is appropriate. Galaxy-dev is generally used for development topics.
http://wiki.g2.bx.psu.edu/Support#Mailing_Lists

Thanks!
Jen
Galaxy team

On 7/16/12 6:57 AM, Irene Bassano wrote:
Hi guys,
I'm new wth NGS and have few basic questions about Galaxy for RNAseq:
1. when I run Cufflinks on my TopHat accepted hits, WHEN and WHY do i have to 
chose a reference annotation?Results are obviously different
2.if i chose this option, which one of the 2 references I have to upload from 
UCSC: RefSeq Genes or Knowngenes (both under Gene and genes prediction tracks).

Hope anyone can help

Thanks
ib

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