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