ChIP-seq: strand shifts

Cited from the book "Tag-based Next Generation Sequencing" page 146-147.

For single-end ChIP-seq, there should be an enrichment of sequence reads on the positive and negative strand flanking the location of a true protein interaction site. The sequence reads from the positive and negative strands can be shifted or extended to construct a combined read density profile.

In a single-end ChIP-seq experiment, sequence reads from the positive and negative strands are usually shifted or extended towards its 3' end by a certain number of bases (usually half the estimated average fragment length) such that the location with the highest read density corresponds to the center of the ChIP protected region. One way to estimate the optimal "shift distance" is by analyzing the strand cross-correlation profile.