I changed the minimum alignment count to: 100, 400, and 1000
minimum alignment differential expressed genes 100 4, 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?