Is anyone experienced in using bamCompare from deeptools? I ran it to compare a ChIP sample to its input, using SES normalization, outputting the log2 ratio. If I do the same on a replicate with its own input, can I then directly compare the log2 ratios for the two outputs in a certain region (or the genome), e.g. for a sample-to-sample correlation plot?
bamCompare -e 200 -bs 1 --scaleFactorsMethod SES -o out_log2ratio.bigwig -b1 sample.bam -b2 input.bam