Mercurial > repos > bgruening > hicexplorer_hicfindtads

comparison hicFindTADs.xml @ 4:8b60271e7e54 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author iuc
date Sat, 16 Dec 2017 16:32:17 -0500
parents a9c1d76b90c4
children db2cc9e1ff76
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3:f569cd2afecb 4:8b60271e7e54
109 <output name="tad_score" file="find_TADs/multiFDR_tad_score.bm" ftype="bedgraph" compare="sim_size" delta="35000" /> 109 <output name="tad_score" file="find_TADs/multiFDR_tad_score.bm" ftype="bedgraph" compare="sim_size" delta="35000" />
110 <output name="matrix_output" file="find_TADs/multiFDR_zscore_matrix.h5" ftype="h5" compare="sim_size" delta="50000" /> 110 <output name="matrix_output" file="find_TADs/multiFDR_zscore_matrix.h5" ftype="h5" compare="sim_size" delta="50000" />
111 </test> 111 </test>
112 </tests> 112 </tests>
113 <help><![CDATA[ 113 <help><![CDATA[
114 Calculate TADs
115 ==============
114 116
115 **What it does** 117 Topological associated domains (TADs) are regions on the DNA which tend to interact within the region a lot, but not outside their boundaries. More information_.
116 118
117 Uses the graph clustering measure "conductance" to find minimum cuts that correspond to boundaries. 119 Calculation
120 ------------
121 ``hicFindTADs`` computes the TAD regions in two steps: In a first step it computes a TAD-separation score based on a z-score matrix for all bins. The z-score is defined as:
118 122
123 “The absolute value of z represents the distance between the raw score and the population mean in
124 units of the standard deviation. z is negative when the raw score is below the mean, positive when above.”
125 [Source_].
126
127 .. image:: $PATH_TO_IMAGES/z-score.svg
128 :width: 150
129
130 `Source of image <https://wikimedia.org/api/rest_v1/media/math/render/svg/5ceed701c4042bb34618535c9a902ca1a937a351>`_
131
132 In our case the distribution describes the counts per bin of a genomic distance. In a second step the local minima of the TAD-separation score is evaluated with respect to the surrounding bins to assign a p-value. Two multiple testing corrections can be applied to filter the results: `Bonferroni <https://en.wikipedia.org/wiki/Bonferroni_correction>`_ or the `false discovery rate <https://en.wikipedia.org/wiki/False_discovery_rate>`_.
133
134
135 Input
136 -----
137
138 Parameters
139 __________
140 - contact matrix to compute the TADs on
141 - minimum window length
142 - maximum window length
143 - step size
144 - multiple testing correction
145 - minimum threshold
146 - minimum distance
147
148
149 hicFindTADs tries to identify sensible parameters but those can be change to identify more stringent set of boundaries.
150
151 Output
152 ------
153
154 - Boundary positions as a bed file
155 - Matrix with multi-scale TAD scores as a bedgraph
156 - TAD domains as a bed file
157 - Boundary information plus score as gff
158 - TAD information in bm file
159 - Z-score matrix in h5
160
161 The calulated TAD regions can be plotted with ``hicPlotTADs``.
162
163
164 .. image:: $PATH_TO_IMAGES/master_TADs_plot.png
165 :width: 80 %
166
167
168
169 For more information about HiCExplorer please consider our documentation on readthedocs.io_
170
171 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
172 .. _Source: https://en.wikipedia.org/wiki/Standard_score#Calculation_from_raw_score
173 .. _information: https://en.wikipedia.org/wiki/Topologically_associating_domain_
119 ]]></help> 174 ]]></help>
120 <expand macro="citations" /> 175 <expand macro="citations" />
121 </tool> 176 </tool>