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Commit message:
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04 |
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modified:
hicFindTADs.xml macros.xml |
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added:
static/images/SRR027956.svg static/images/SRR0279XX_perChr_eigenvector1.png static/images/diagnostic_plot.png static/images/hicCorrelate_pearson.png static/images/hicCorrelate_pearson_scatter.png static/images/hicCorrelate_spearman.png static/images/hicCorrelate_spearman_scatter.png static/images/hicPlotDistVsCounts_result1.png static/images/hicPlotDistVsCounts_result2.png static/images/hicQC.png static/images/master_TADs_plot.png static/images/z-score.svg |
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| diff -r f569cd2afecb -r 8b60271e7e54 hicFindTADs.xml --- a/hicFindTADs.xml Mon Nov 27 11:12:30 2017 -0500 +++ b/hicFindTADs.xml Sat Dec 16 16:32:17 2017 -0500 |
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| @@ -111,11 +111,66 @@ </test> </tests> <help><![CDATA[ +Calculate TADs +============== -**What it does** +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_. + +Calculation +------------ +``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: + +“The absolute value of z represents the distance between the raw score and the population mean in +units of the standard deviation. z is negative when the raw score is below the mean, positive when above.” +[Source_]. + +.. image:: $PATH_TO_IMAGES/z-score.svg + :width: 150 + +`Source of image <https://wikimedia.org/api/rest_v1/media/math/render/svg/5ceed701c4042bb34618535c9a902ca1a937a351>`_ + +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>`_. + + +Input +----- -Uses the graph clustering measure "conductance" to find minimum cuts that correspond to boundaries. +Parameters +__________ +- contact matrix to compute the TADs on +- minimum window length +- maximum window length +- step size +- multiple testing correction +- minimum threshold +- minimum distance + + +hicFindTADs tries to identify sensible parameters but those can be change to identify more stringent set of boundaries. + +Output +------ +- Boundary positions as a bed file +- Matrix with multi-scale TAD scores as a bedgraph +- TAD domains as a bed file +- Boundary information plus score as gff +- TAD information in bm file +- Z-score matrix in h5 + +The calulated TAD regions can be plotted with ``hicPlotTADs``. + + +.. image:: $PATH_TO_IMAGES/master_TADs_plot.png + :width: 80 % + + + +For more information about HiCExplorer please consider our documentation on readthedocs.io_ + +.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html +.. _Source: https://en.wikipedia.org/wiki/Standard_score#Calculation_from_raw_score +.. _information: https://en.wikipedia.org/wiki/Topologically_associating_domain_ ]]></help> <expand macro="citations" /> </tool> |
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| diff -r f569cd2afecb -r 8b60271e7e54 macros.xml --- a/macros.xml Mon Nov 27 11:12:30 2017 -0500 +++ b/macros.xml Sat Dec 16 16:32:17 2017 -0500 |
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| @@ -21,7 +21,7 @@ </xml> <xml name="colormap"> - <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/"> + <param argument="--colorMap" name="colormap" type="select" optional="True" label="Color map to use for the heatmap" help=" Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html"> <option value="RdYlBu">RdYlBu</option> <option value="Accent">Accent</option> <option value="Spectral">Spectral</option> |
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| diff -r f569cd2afecb -r 8b60271e7e54 static/images/SRR027956.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/SRR027956.svg Sat Dec 16 16:32:17 2017 -0500 |
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