ChIP-seq: Why MACS doesn't apply tag shifting to the control sample?

Question

[salamandra]

If I understand right, MACS shifts chip-seq tags of a fragment into 3´end because the tags are just small sequences in the extremes of the fragment. But why does it only apply to the ChIP sample and not to the control samples (input DNA)? Or paired-end sequencing isn't done in control samples?

Ref: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-9-r137

Answer 1

[ghostforever.shi]

With a control, MACS will do the peak calling in both sample(test and input) and count the FDR according to the result of two samples' peak calling, which means, in my opinion, tag shifting will be applied to both samples.