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!
What is the ultimate goal that you need these values for? There are for sure alternative approaches that will work. Did you try using the enrichment or significance scores from a peak caller such as
MACS2
for your analysis?