Mercurial > repos > bgruening > hicexplorer_hicmergematrixbins

annotate hicMergeMatrixBins.xml @ 9:90645548f8cc draft

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author iuc
date Sat, 09 Jun 2018 15:36:26 -0400
parents c14ba4629233
children 49c8055f6830
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1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>merge adjacent bins from a Hi-C contact matrix to reduce its resolution</description>
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3 <macros>
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4 <token name="@BINARY@">hicMergeMatrixBins</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 hicMergeMatrixBins
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10 --matrix '$matrix_h5_cooler'
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11 --numBins $numBins
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12 $runningWindow
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13 --outFileName matrix.$outputFormat
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14 && mv matrix.$outputFormat matrix
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16 ]]>
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17 </command>
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18 <inputs>
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19 <expand macro='matrix_h5_cooler_macro' />
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20
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21 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
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22 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." />
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23 <param name='outputFormat' type='select' label="Output file format">
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24 <option value='h5' selected='true'>HiCExplorer format</option>
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25 <option value="cool">cool</option>
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26 </param>
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27 </inputs>
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28 <outputs>
5
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29 <data name="outFileName" from_work_dir="matrix" format="h5">
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30 <change_format>
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31 <when input="outputFormat" value="cool" format="cool" />
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32 </change_format>
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33 </data>
0
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
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38 <param name="numBins" value="5" />
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39 <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43
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44 Change matrix resolution
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45 ========================
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47 **hicMergeMatrixBins** is used to decrease the resolution of a matrix. With this tool, you can for example create out of a 100 kb
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48 contact matrix a 1000 kb one:
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50 Number of bins to merge = 10
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52 100 kb * 10 = 1000 kb = 1 Mb
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54 Depending on the downstream analyses to perform on a Hi-C matrix generated with HiCExplorer, one might need different bin resolutions. For example using ``hicPlotMatrix`` to display chromatin interactions of a whole chromosome will not produce any meaningful vizualisation if it is performed on a matrix at restriction sites resolution (unmerged). Furthermore, the higher the resolution of a matrix, the more detailed it is, which can make it
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55 difficult to interpret, especially if the read depth of the Hi-C data is not high enough. **hicMergeMatrixBins** address these issues by merging a given number of adjacent bins to reduce Hi-C matrices resolution.
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57 _________________
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59 Usage
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60 -----
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62 To limit the loss of information, it is mandatory to perform **hicMergeMatrixBins** on matrices prior to any correction and any other bin merging (direct output from ``hicBuildMatrix``). After bin merging, ``hicCorrectMatrix`` must be used for downstream analyses requiring corrected matrices.
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64 _________________
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66 Output
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67 ------
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69 **hicMergeMatrixBins** outputs a Hi-C matrix with reduced resolution.
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71 Below, we will develop the example of a Hi-C matrix in *Drosophila melanogaster* that we want to display at the whole X-chromosome scale and at the scale of a 1Mb region of the X chromosome. To do this, we performed two different bin merging using **hicMergeMatrixBins** on an uncorrected matrix built at the restiction sites resolution using ``hicBuildMatrix``.
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73 Starting from a matrix with bins of a median length of 529bp (restriction enzyme resolution, here DpnII), running **hicMergeMatrixBins** with a number of bins to merge of 3 produced a matrix with bins of a median length of 1661bp, while **hicMergeMatrixBins** with a number of bins to merge of 50 produced a matrix with bins of a median length of 29798bp.
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75 After the correction of these three matrices using ``hicCorrectMatrix``, we plotted them using ``hicPlotMatrix`` at the scale of the whole X-chromosome and at the scale of the X:2000000-3000000 region to see the effect of bin merging on the interactions visualization.
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77 - **Effect of bins merging at the scale of a chromosome:**
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79 .. image:: $PATH_TO_IMAGES/hicMergeMatrixBins_Xchr.png
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80 :width: 60 %
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82 When observed altogether, the plots above show that the merging of bins by 50 is the most adequate way to plot interactions for a whole chromosome in *Drosophila melanogaster* when starting from a matrix with bins of a median length of 529bp.
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83
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84 - **Effect of bins merging at the scale of a specific region:**
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85
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86 .. image:: $PATH_TO_IMAGES/hicMergeMatrixBins_Xregion.png
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87 :width: 60 %
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88
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89 When observed altogether, the plots above show that the merging of bins by 3 is the most adequate way to plot interactions for a region of 1Mb in Drosophila melanogaster when starting from a matrix with bins of a median length of 529bp.
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90
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91 _________________
2
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92
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93 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
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94
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95 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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96 ]]></help>
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97 <expand macro="citations" />
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98 </tool>