[galaxy-user] correct input into the minimum alignment count

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