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


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