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comparison hicMergeMatrixBins.xml @ 7:c14ba4629233 draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
author iuc
date Fri, 27 Apr 2018 03:38:09 -0400
parents 8926550196ce
children 49c8055f6830
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6:8926550196ce 7:c14ba4629233
1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>Merges bins from a Hi-C matrix</description> 2 <description>merge adjacent bins from a Hi-C contact matrix to reduce its resolution</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicMergeMatrixBins</token> 4 <token name="@BINARY@">hicMergeMatrixBins</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
17 </command> 17 </command>
18 <inputs> 18 <inputs>
19 <expand macro='matrix_h5_cooler_macro' /> 19 <expand macro='matrix_h5_cooler_macro' />
20 20
21 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" /> 21 <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
22 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" /> 22 <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." />
23 <param name='outputFormat' type='select' label="Output file format"> 23 <param name='outputFormat' type='select' label="Output file format">
24 <option value='h5' selected='true'>HiCExplorer format</option> 24 <option value='h5' selected='true'>HiCExplorer format</option>
25 <option value="cool">cool</option> 25 <option value="cool">cool</option>
26 </param> 26 </param>
27 </inputs> 27 </inputs>
42 <help><![CDATA[ 42 <help><![CDATA[
43 43
44 Change matrix resolution 44 Change matrix resolution
45 ======================== 45 ========================
46 46
47 ``hicMergeMatrixBins`` is used to decrease the resolution of a matrix. With this tool you can create out of a 100 kb 47 **hicMergeMatrixBins** is used to decrease the resolution of a matrix. With this tool, you can for example create out of a 100 kb
48 contact matrix a 1000 kb one: 48 contact matrix a 1000 kb one:
49 49
50 Number of bins to merge = 10 50 Number of bins to merge = 10
51 51
52 100 kb * 10 = 1000 kb = 1 Mb 52 100 kb * 10 = 1000 kb = 1 Mb
53 53
54 This functionality is useful especially for plotting. The higher the resolution of an contact matrix is, the more likely it is 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
55 to run out of memory while plotting. This is caused by the circumstances that we compute internally with a sparse matrices but 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.
56 to plot we need a dense one. Furthermore, the higher the resolution of a matrix the more detailed it is which can make it
57 difficult to interpret, especially if the read depth of the Hi-C data is not high.
58 56
59 Input 57 _________________
58
59 Usage
60 ----- 60 -----
61 61
62 Parameters 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.
63 __________ 63
64 - contact matrix to change the resolution on 64 _________________
65 - Number of bins to merge
66 - running window
67 65
68 Output 66 Output
69 ------ 67 ------
70 68
71 A contact matrix with the resolution ``original resolution * number of bins``. 69 **hicMergeMatrixBins** outputs a Hi-C matrix with reduced resolution.
70
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``.
72
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.
74
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.
76
77 - **Effect of bins merging at the scale of a chromosome:**
78
79 .. image:: $PATH_TO_IMAGES/hicMergeMatrixBins_Xchr.png
80 :width: 60 %
81
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.
83
84 - **Effect of bins merging at the scale of a specific region:**
85
86 .. image:: $PATH_TO_IMAGES/hicMergeMatrixBins_Xregion.png
87 :width: 60 %
88
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.
90
91 _________________
72 92
73 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 93 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
74 94
75 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 95 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
76 ]]></help> 96 ]]></help>