# HG changeset patch # User iuc # Date 1513459937 18000 # Node ID 8b60271e7e5494d47bc746f892f969a0aaee1aec # Parent f569cd2afecb2182302de905cabfb8811e895cb0 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04 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 @@ -111,11 +111,66 @@ `_ + +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 `_ or the `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_ ]]> 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 @@ -21,7 +21,7 @@ - + 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 @@ -0,0 +1,678 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r f569cd2afecb -r 8b60271e7e54 static/images/SRR0279XX_perChr_eigenvector1.png Binary file static/images/SRR0279XX_perChr_eigenvector1.png has changed diff -r f569cd2afecb -r 8b60271e7e54 static/images/diagnostic_plot.png Binary file static/images/diagnostic_plot.png has changed diff -r f569cd2afecb -r 8b60271e7e54 static/images/hicCorrelate_pearson.png Binary file static/images/hicCorrelate_pearson.png has changed diff -r f569cd2afecb -r 8b60271e7e54 static/images/hicCorrelate_pearson_scatter.png Binary file static/images/hicCorrelate_pearson_scatter.png has changed diff -r f569cd2afecb -r 8b60271e7e54 static/images/hicCorrelate_spearman.png Binary file static/images/hicCorrelate_spearman.png has changed diff -r f569cd2afecb -r 8b60271e7e54 static/images/hicCorrelate_spearman_scatter.png Binary file static/images/hicCorrelate_spearman_scatter.png has changed diff -r f569cd2afecb -r 8b60271e7e54 static/images/hicPlotDistVsCounts_result1.png Binary file static/images/hicPlotDistVsCounts_result1.png has changed diff -r f569cd2afecb -r 8b60271e7e54 static/images/hicPlotDistVsCounts_result2.png Binary file static/images/hicPlotDistVsCounts_result2.png has changed diff -r f569cd2afecb -r 8b60271e7e54 static/images/hicQC.png Binary file static/images/hicQC.png has changed diff -r f569cd2afecb -r 8b60271e7e54 static/images/master_TADs_plot.png Binary file static/images/master_TADs_plot.png has changed diff -r f569cd2afecb -r 8b60271e7e54 static/images/z-score.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/z-score.svg Sat Dec 16 16:32:17 2017 -0500 @@ -0,0 +1,27 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file