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normalizeUsing in parserCommon: None = first explained
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‎pydeeptools/deeptools/parserCommon.py‎

Lines changed: 2 additions & 2 deletions
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@@ -231,7 +231,8 @@ def normalization_options():
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group.add_argument('--normalizeUsing',
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help='Use one of the entered methods to '
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'normalize the number of reads per bin. By default, no normalization is performed. '
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'normalize the number of reads per bin.'
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'None = the default and equivalent to not setting this option at all. '
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'RPKM = Reads Per Kilobase per Million mapped reads; '
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'CPM = Counts Per Million mapped reads, same as CPM in RNA-seq; '
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'BPM = Bins Per Million mapped reads, same as TPM in RNA-seq; '
@@ -245,7 +246,6 @@ def normalization_options():
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'sum of all reads per bin (in millions). '
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'RPGC (per bin) = number of reads per bin / '
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'scaling factor for 1x average coverage. '
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'None = the default and equivalent to not setting this option at all. '
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'This scaling factor, in turn, is determined from the '
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'sequencing depth: (total number of mapped reads * fragment length) / '
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'effective genome size.\nThe scaling factor used '

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