I am using spp peak caller to extract estimated fragment size and ChIP QC metrics (RSC and NSC values) on my ChIP seq samples. I am using "phantompeakqualtools" for performing the spp peak calling.

Upon performing run_spp.R on the test.bam files I got the following results. I performed with default parameters (A) and (B) Changed the parameter in strand shift (break changed from 5 to 1, Here I am attaching the two plots discussed in question). I observed in plot B the cross-correlation is maximum at a negative value. I couldn't infer the result?

Can anyone help me to understand the need for a negative strand-shift value in peak calling with spp?

Thank you