My ChIP-seq experiment had no input due to practical reasons. So I don't have access to this pipeline at the moment?

no input? so no files?

I guess in this case the "input" is the control sample and if it is mandatory the analysis cannot be done with the pipeline

Thank you for your reply. I really don't have "control" sample, which looks like a bad situation.

maybe you could try the cutandrun pipeline... due to much lower background it can be performed without input and so it is not mandatory for the pipeline ...then of course the reliability of results is a big question... I hope that at least you have biological replicates otherwise the situation can be quite bad indeed