Answers.Body: <p>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.</p>
  <p>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.
  <a href="https://genome.cshlp.org/content/22/9/1813.full.pdf" rel="nofollow noreferrer">https://genome.cshlp.org/content/22/9/1813.full.pdf</a></p>
  <p><a href="https://i.sstatic.net/2ioYL.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/2ioYL.png" alt="x-axis: genomic position; y-axis: read density" /></a>
  <a href="https://i.sstatic.net/2mM3P.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/2mM3P.png" alt="x-axis: genomic position; y-axis: read density" /></a></p>
  
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Answers.Text: i'm not sure what the best terms are for strands -- "positive"/"negative"; "watson"/"crick"?
Answers.UserDisplayName: eric_kernfeld
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Answers.Text: I think positive / negative (as you have here) is reasonable, especially as it relates to gene-relative direction.
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Answers.Text: Positive/negative, sense/antisense, top/bottom, forward/reverse, plus/minus... All describe the same thing.
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Body: <p>I've seen two uses of this term that seem to refer to completely different phenomena. Is my understanding correct?</p>
  
  <ol>
  <li>In Jain et al. "Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments" (<a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4538825/" rel="nofollow noreferrer">PMC4538825</a>), 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.</li>
  <li>The ENCODE quality metrics (<a href="https://genome.ucsc.edu/ENCODE/qualityMetrics.html#chipSeq" rel="nofollow noreferrer">link</a>) 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.)</li>
  </ol>
  
Tags: <chip-seq>
Title: What are phantom peaks in ChIP-seq?
ThreadText: # What are phantom peaks in ChIP-seq?
  
  (Asked by: username_0 on 2018-04-27)
  
  I've seen two uses of this term that seem to refer to completely different phenomena. Is my understanding correct?
  
  1. In Jain et al. "Active promoters give rise to false positive ‘Phantom Peaks’ in ChIP-seq experiments" ([PMC4538825](https://www.ncbi.nlm.nih.gov/pmc/articles/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.
  2. The ENCODE quality metrics ([link](https://genome.ucsc.edu/ENCODE/qualityMetrics.html#chipSeq)) 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.)
  
  **Tags:** chip-seq
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2020-08-31. Score: 1
  
  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., ... & 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>
  
  [![x-axis: genomic position; y-axis: read density](https://i.sstatic.net/2ioYL.png)](https://i.sstatic.net/2ioYL.png)
  [![x-axis: genomic position; y-axis: read density](https://i.sstatic.net/2mM3P.png)](https://i.sstatic.net/2mM3P.png)
  
  > **Comments:**
  > **username_0**: i'm not sure what the best terms are for strands -- "positive"/"negative"; "watson"/"crick"?  
  > **username_1**: I think positive / negative (as you have here) is reasonable, especially as it relates to gene-relative direction.  
  > **username_2**: Positive/negative, sense/antisense, top/bottom, forward/reverse, plus/minus... All describe the same thing.  
  
  ---
  
  