Changes between Version 45 and Version 46 of SOPs/chip_seq_peaks

Timestamp:

08/23/18 09:28:37 (6 years ago)

Author:

gbell

Comment:

--

SOPs/chip_seq_peaks

@@ -28 +28 @@
 }}}
   * ENCODE recommends normalized strand coefficientt (NSC) > 1.05 and relative strand correlation (RSC) > 0.08  [[https://genome.cshlp.org/content/genome/22/9/1813.full.html#boxed-text-3 | Ref]]
-  * After this analysis a good ChIP-seq experiment will have a second peak (reflecting the fragment size) at least as tall as the first peak (reflecting read length). This is how the graph should look: ([[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/figure/F4/|Fig4E]]). If the second peak is smaller than the first, ([[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/figure/F4/|like the example shown in Fig4G Marginal]]),  macs will not estimate fragment size correctly. In that case we recommend running macs with parameters "--nomodel" and "--shiftsize=half_of_the_fragment_size", or "--nomodel" and "--extsize=fragment_size". The fragment size is detected on the strand cross correlation analysis.
+  * After this analysis a good ChIP-seq experiment will have a second peak (reflecting the fragment size) at least as tall as the first peak (a "phantom" peak reflecting read length). This is how the graph should look: ([[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/figure/F4/|Fig4E]]). If the second peak is smaller than the first, ([[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431496/figure/F4/|like the example shown in Fig4G Marginal]]),  macs will not estimate fragment size correctly. In that case we recommend running macs with parameters "--nomodel" and "--shiftsize=half_of_the_fragment_size", or "--nomodel" and "--extsize=fragment_size". The fragment size is detected on the strand cross correlation analysis.
  
 === Step 3: Call peaks (presumed bound regions), especially for transcription factors ===