Mercurial > repos > bgruening > hicexplorer_hiccorrectmatrix

comparison hicCorrectMatrix.xml @ 4:b55d7936cbe0 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 16:35:10 -0500
parents ecf11dda45f7
children 44919af9194b
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3:33064489fb8a 4:b55d7936cbe0
142 <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/> 142 <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/>
143 </test> 143 </test>
144 </tests> 144 </tests>
145 <help><![CDATA[ 145 <help><![CDATA[
146 146
147 **What it does** 147 Matrix correction
148 148 ==================
149 Runs Dekker's iterative correction over a Hi-C matrix. 149
150 150 | ``hicCorrectMatrix`` runs Dekker's iterative correction over a Hi-C matrix (`Imakaev 2012`_.). For correcting the matrix,
151 correct: Run the iterative correction. 151 | it is important to remove the unassembled scaffolds (e.g. `NT_`), mitochondrial DNA and Y chromosome and keep only
152 152 | chromosomes, as scaffolds create problems with matrix correction. Therefore
153 diagnostic_plot: Plots a histogram of the coverage per bin together with the 153 | we use the chromosome names (1-19, X, Y) here.
154 |
155 | **Important**: Use ‘chr1 chr2 chr3 etc.’ if your genome index uses chromosome names with the ‘chr’ prefix.
156
157 Matrix correction works in two steps: first a histogram containing the sum of contact per bin (row sum) is produced. This plot needs to be inspected to decide the best threshold for removing bins with lower number of reads. The second steps removes the low scoring bins and does the correction.
158
159 Input
160 -----
161
162
163 Diagnostic plot
164 ~~~~~~~~~~~~~~~~
165 Plots a histogram of the coverage per bin together with the
154 modified z-score based on the median absolute deviation 166 modified z-score based on the median absolute deviation
155 method (see Boris Iglewicz and David Hoaglin 1993, Volume 167 method.
156 16: How to Detect and Handle Outliers The ASQC Basic 168
157 References in Quality Control: Statistical Techniques, 169 See Boris Iglewicz and David Hoaglin 1993, Volume 16:
170 How to Detect and Handle Outliers The ASQC Basic References in Quality Control: Statistical Techniques,
158 Edward F. Mykytka, Ph.D., Editor. 171 Edward F. Mykytka, Ph.D., Editor.
159 172
173 Parameters
174 __________
175 - the contact matrix
176 - Max value for the x-axis in counts per bin
177 - include chromosomes
178
179
180 Correct
181 ~~~~~~~
182
183 Run the iterative correction.
184
185 Parameters
186 __________
187 - number of iterations
188 - inflation cutoff
189 - trans region cutoff
190 - sequenced count cutoff
191 - skip diagonal counts
192 - normalize each chromosome separately
193 - remove bins of low coverage
194 - remove bins of large coverage
195 - include chromosomes
196
197 Output
198 ------
199
200 Diagnostic plot:
201
202 .. image:: $PATH_TO_IMAGES/diagnostic_plot.png
203 :width: 70%
204
205 Correct:
206 - the corrected contact matrix
207
208 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
209
210 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
211
212 .. _`Imakaev 2012`: http://doi.org/doi:10.1038/nmeth.2148
160 ]]></help> 213 ]]></help>
161 <expand macro="citations" /> 214 <expand macro="citations" />
162 </tool> 215 </tool>
163 216