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