Mercurial > repos > bgruening > deeptools
comparison computeGCBias.xml @ 24:d7c9fd76e41e draft
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author | bgruening |
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date | Tue, 04 Feb 2014 09:12:07 -0500 |
parents | 8c452f37c896 |
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23:8c452f37c896 | 24:d7c9fd76e41e |
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110 </outputs> | 110 </outputs> |
111 <help> | 111 <help> |
112 | 112 |
113 **What it does** | 113 **What it does** |
114 | 114 |
115 This tool computes the GC bias using the method proposed by Benjamini and Speed (2012). Nucleic Acids Res. (see below for more explanations) | 115 This tool computes the GC bias using the method proposed by Benjamini and Speed (2012) Nucleic Acids Res. (see below for more explanations) |
116 The output is used to plot the bias and can also be used later on to correct the bias with the tool correctGCbias. | 116 The output is used to plot the bias and can also be used later on to correct the bias with the tool correctGCbias. |
117 There are two plots produced by the tool: a boxplot showing the absolute read numbers per genomic-GC bin and an x-y plot | 117 There are two plots produced by the tool: a boxplot showing the absolute read numbers per genomic-GC bin and an x-y plot |
118 depicting the ratio of observed/expected reads per genomic GC content bin. | 118 depicting the ratio of observed/expected reads per genomic GC content bin. |
119 | 119 |
120 ----- | 120 ----- |
130 usually shows a significant bias towards reads with high GC content (>50%) | 130 usually shows a significant bias towards reads with high GC content (>50%) |
131 | 131 |
132 .. image:: $PATH_TO_IMAGES/QC_GCplots_input.png | 132 .. image:: $PATH_TO_IMAGES/QC_GCplots_input.png |
133 | 133 |
134 | 134 |
135 You can find more details in the `computeGCBias wiki`_. | 135 You can find more details on the computeGCBias wiki page: computeGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias |
136 | |
137 .. _computeGCBias wiki: https://github.com/fidelram/deepTools/wiki/QC#wiki-computeGCbias | |
138 | 136 |
139 | 137 |
140 **Output files**: | 138 **Output files**: |
141 | 139 |
142 - Diagnostic plot | 140 - Diagnostic plot |