Mercurial > repos > bgruening > hicexplorer_hiccomparematrices

comparison hicCompareMatrices.xml @ 1:08e157ceda6f 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 03:33:16 -0400
parents a0ab04565c73
children 6d2c4187805b
comparison
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0:a0ab04565c73 1:08e157ceda6f
1 <tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0"> 1 <tool id="hicexplorer_hiccomparematrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>normalize and compare two HiC matricies</description> 2 <description>normalize and compare two Hi-C contact matrices</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">hicCompareMatrices</token> 4 <token name="@BINARY@">hicCompareMatrices</token>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
54 <output name="outFileName" file="compare_matrices_pearson_ratio.cool" ftype="cool" compare="sim_size" delta='2000'/> 54 <output name="outFileName" file="compare_matrices_pearson_ratio.cool" ftype="cool" compare="sim_size" delta='2000'/>
55 </test> 55 </test>
56 56
57 </tests> 57 </tests>
58 <help><![CDATA[ 58 <help><![CDATA[
59 Comparison of HiC matrices 59 Comparison of Hi-C matrices
60 ========================== 60 ===========================
61 `hicCompareMatrices` takes two matrices, normalizes them and appliesthe given operation. To
62 normalize the matrices each element is divided by sum of the matrix.
63 61
64 Input 62 This tool is useful to compare two matrices by applying operations like difference, ratio or log2ratio after normalization. To
63 normalize the matrices, each element is divided by the sum of the matrix.
64
65 **hicCompareMatrices** can be used for example to determine the effect of a mutation compared to wild-type samples on contact enrichment,
66 or to see TAD structure modifications near differentially expressed genes between two conditions when followed by ``hicPlotMatrix``.
67 It can also be used to compare two biological replicates.
68
69 _________________
70
71 Usage
65 ----- 72 -----
66 - the matricies to be compared
67 73
74 **hicCompareMatrices** is usually perfomed on corrected matrices (``hicCorrectMatrix``) with bins merged (``hicMergeMatrixBins``) depending
75 on the downstream analyses to perform (visualisation of a whole chromosome, or of a small region, etc).
68 76
77 _________________
78
79 Output
80 ------
81
82 Here is an example of a log2ratio comparison between M1BP Knockdown and GST cells in
83 *Drosophila melanogaster* on corrected matrices with 50 bins merged (about 30kb bins) plotted using ``hicPlotMatrix``.
84
85 .. image:: $PATH_TO_IMAGES/hicCompareMatrices_m1bp_over_gst_log2_m50_matrix_plot.png
86 :width: 50%
87
88 In this plot we see that the cells with a M1BP Knockdown display a negative log2ratio compared to the wild-type. Depletion of M1BP thus show a dramatic effect on the distribution of Hi-C contacts in which short range contacts decrease (Ramirez *et al.* 2017, High-resolution TADs reveal DNA sequences underlying genome organization in flies, https://doi.org/10.1038/s41467-017-02525-w).
89
90 Below you can find an example of a log2ratio plot between Hi-C matrices of two biological replicates, no differences are observable which means that the replicates are well correlated.
91
92 .. image:: $PATH_TO_IMAGES/hicCompareMatrices_QC_log2_m50_matrix_plot.png
93 :width: 50%
94
95 _________________
69 96
70 | For more information about HiCExplorer please consider our documentation on readthedocs.io_ 97 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
71 98
72 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html 99 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
73 ]]></help> 100 ]]></help>