What are phantom peaks in ChIP-seq? I've seen two uses of this term that seem to refer to completely different phenomena. Is my understanding correct?


In Jain et al. "Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments" (PMC4538825), a phantom peak is a region on the genome where lots of reads align in a control experiment where there is none of the protein being IP'd, but not in a control experiment without any antibody. The authors (speculatively) attribute this to general stickiness of transcription factors and the transcriptional machinery, which can bind with potentially any antibody and get IP'd.
The ENCODE quality metrics (link) say "a cross-correlation phantom-peak is ... observed at a strand-shift equal to the read length." They are referring to a high correlation of x[i] and y[i + r] where r is the read length, x[i] contains counts of tags aligning to the Watson strand at coordinate i, and y[i+r] contains counts of tags aligning to the Crick strand at coordinate i+r. They attribute this phenomenon to variations in mappability. (I don't understand their explanation at all, but that's a separate question.)
This is almost right, but it's missing a little context. In ChIP-seq, it's typical to shift the positive and negative reads because otherwise the peaks end up offset from each other. The amount of shift is determined by trying different shifts and measuring how well the read densities correlate between positive and negative strands. In the question, the first sense talks about a peak on the plot of read density vs genomic position. The second has different x and y axes because it's talking about the cross-correlation between strands. X is the offset between positive and negative strands, and y is the correlation observed at that offset. Look at figures 4D,E in this ENCODE paper for visuals.
Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., ... &amp; Chen, Y. (2012). ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome research, 22(9), 1813-1831.
https://genome.cshlp.org/content/22/9/1813.full.pdf