Difference between Diffbind library size normalisation vs DESeq2 library size normalisation about chip-seq-analysis HOT 2 CLOSED

One probable solution could be, in DESeq2, feeding the total mapped readcount numbers as an extra column and keep it as continuous variable, and incorporate that column in design matrix. So that the raw counts would have the normalisation affect from BAM library size also. Does it sound logical?

from chip-seq-analysis.

I missed this issue. I think either using the total library size (from bam file) or using only the reads fall into peaks (DESeq2) should be fine. I have not tested that. If you do both and compare, do you see big differences? especially for discrepant differential peaks, you may want to visualize in IGV and judge yourself.

from chip-seq-analysis.