Dear all, I changed the minimum alignment count to: 100, 400, and 1000
minimum alignment differential expressed genes 100 4, 000 400 2,000 1000 (default) 1,000 I was wondering, which minimum alignment we should go with? It would appear the higher the alignment, the amount of differential expressed genes are decreased. I was also wondering if the minimum alignment refers to the # of reads per sequence? Is this true? Also how are the FPKM and the minimum alignment are related? Thanks, Bao ___________________________________________________________ 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: http://lists.bx.psu.edu/