I am looking for advice on how to appropriately subtract background signal from true signal before performing analysis with DESeq2.
I've performed a cut-and-run experiment, which is akin to ChIP-Seq and reveals protein-genome interactions. The technique results in background signal at locations where DNA is less protected, and this background can obscure signal from bonafide interactions - such as when performing DE analysis (I say DE, but we are talking about differential binding here).
My protein is recruited to DNA downstream of other proteins. To quantify the amount of non-specific background signal, I degraded an upstream protein and then performed cut-and-run. Signal remained throughout the genome - this represents non-specific background signal. Background is often large relative to a gain in signal in response to treatment, and so these changes are often obscured when performed DE analysis . Luckily, the amount of signal appears to be reproducible (low variation between replicates).
I quantified gene-counts with Salmon. For each gene, I intend to subtract the average background signal away from average total signal. However, I am unsure if this would be appropriate because Salmon does more than a simple read count.
After subtracting out background signal, I intend to use the counts data in DESeq2 analysis.
Thanks for any advice.