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Add updated CCF plots to CD4 examples

Ryan C. Thompson 8 years ago
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762ecd8f04

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examples/Salomon/CD4/CCF-max-plot.pdf


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examples/Salomon/CD4/CCF-plots-noBL.pdf


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examples/Salomon/CD4/CCF-plots.pdf


+ 6 - 0
examples/Salomon/CD4/README.mkdn

@@ -51,6 +51,12 @@ and you can view some presentation slides based on this analysis
   size. You can also observe from the periodic wave-like pattern,
   indicating that multiple adjacent histones tend to share the same
   histone modification.
+- [`CCF-plots-noBL.pdf`](CCF-plots-noBL.pdf) show the same plots, but
+  without removing reads in so-called "blacklist" regions that
+  typically contain high-coverage artifact signals. The result is a
+  much messier plot, with many samples having a peak at the read
+  length (dotted line) rather than the actual width of a histone
+  (solid line).
 - [`site-profile-plots.pdf`](site-profile-plots.pdf) shows plots of
   the relative coverage depth profiles around local coverage maxima.
   This plot is used to determine the footprint size of the protein