I am using bamCompare to normalize my Chip-seq data (antibody + input). The reference genome is bigger than 10G, and every chromosome size is bigger than 600M, I run the bamCompare for each chromosome seperately(because there is no big enough memory to do with the whole genome; SES normalization; binsize=50), when I check the results of bamCompare, I found that the log2 ratio in every chromosome site bigger than 538M is 0 (even if I set
--region chr1:500000000:830000000), I didn't find any information on the official website, then what should I do with this? Or is there any other software to calculate log2 ratio? Thanks!