Hello. Does the nf-core/chiseq version 2.0.0 goes until the part when we can get the differential sites between contrasting sample groups or does it went out in this version? I am a little confused on how to set the contrasting sample groups in the sample sheet, if this version is capable of doing it. Can anyone help me?

Hi! For differential analysis you may have a look at a different pipeline, which should work for both RNA-seq and ChIP-seq: https://nf-co.re/differentialabundance/