# HG changeset patch # User iuc # Date 1524814767 14400 # Node ID b05f292d220c82ad5400fe1ef86ce4f31ab4d628 # Parent 43332e51a712557b356b99f496cd83c7becc11de planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8 diff -r 43332e51a712 -r b05f292d220c hicFindTADs.xml --- a/hicFindTADs.xml Wed Mar 07 03:46:54 2018 -0500 +++ b/hicFindTADs.xml Fri Apr 27 03:39:27 2018 -0400 @@ -1,5 +1,5 @@ - find minimum cuts that correspond to boundaries + identify TAD boundaries by computing the degree of separation of each Hi-C matrix bin hicFindTADs macros.xml @@ -8,7 +8,7 @@ + help="This parameter can be used to reduce spurious boundaries caused by noise. "/> - + - + - + @@ -108,69 +108,71 @@ - `_ 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 ------ - -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 +**hicFindTADs** produces multiple outputs: + +- TAD boundaries positions as a BED file and TAD separation score. +- TAD boundaries positions with delta, p-value and TAD separation score as GFF. +- TAD domains as a BED file. +- TAD seperation score as bigwig (bw), bedgraph and numpy array (npz) format. These files can be used to plot the so-called TAD insulation score or TAD separation score along the genome or at specific regions. This score is much more reliable across samples than the number of TADs or the TADs width that can vary depending on the sequencing depth because of the lack of information at certain bins, and depending on the parameters used with this tool. +- Matrix with multi-scale TAD scores as a bed-matrix (bm) file that can be plotted inside ``hicPlotTADs`` to nicely display TAD insulation score alongside Hi-C heatmap and other datasets. +- Z-score matrix in h5 format that is useful to quickly test the --thresholdComparisons, --delta and --correctForMultipleTesting parameters by using the --TAD_sep_score_prefix option pointing to this zscore_matrix.h5 file (will be added in a future update). + +_________________ -The calulated TAD regions can be plotted with ``hicPlotTADs``. +Usage hints +----------- +It is mandatory to test multiple parameters of TAD calling with **hicFindTADs** before making conclusions about the number of TADs in a given sample or before comparing TAD calling between multiple conditions. In order to compare numerous TAD calling parameters at once, it is recommended to use ``hicPlotTADs``, below you can find a plot where multiple TAD calling parameters are displayed for *Drosophila melanogaster* embryos: -.. image:: $PATH_TO_IMAGES/master_TADs_plot.png - :width: 80 % +.. image:: $PATH_TO_IMAGES/hicFindTADs_TAD_calling_comparison.png + :width: 65 % +We can see that the fourth set of **hicFindTADs** parameters with a threshold of 0.001 gives the best results in terms of TAD calling compared to the corrected Hi-C counts distribution and compared to the enrichment of H3K36me3, which is known to be enriched at TAD boundaries in *Drosophila melanogaster*. +_________________ 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 +.. _Source: https://en.wikipedia.org/wiki/Standard_score#Calculation_from_raw_score .. _information: https://en.wikipedia.org/wiki/Topologically_associating_domain_ ]]> diff -r 43332e51a712 -r b05f292d220c involucro Binary file involucro has changed diff -r 43332e51a712 -r b05f292d220c macros.xml --- a/macros.xml Wed Mar 07 03:46:54 2018 -0500 +++ b/macros.xml Fri Apr 27 03:39:27 2018 -0400 @@ -1,7 +1,6 @@ \${GALAXY_SLOTS:-4} - 2.1 - + 2.1.2 #if $use_range.select_use_range == "yes_use_range": --range $range_min:$range_max @@ -28,7 +27,7 @@ - + @@ -40,8 +39,8 @@ - - + + @@ -189,9 +188,9 @@ - + - \${GALAXY_SLOTS:-4} -<<<<<<< HEAD - 2.0 - - - #if $use_range.select_use_range == "yes_use_range": - --range $range_min:$range_max - #end if - - -======= - 2.1alpha1 ->>>>>>> joachimwolff-master - - - hicexplorer - - - @BINARY@ --version - - - - - 10.5281/zenodo.1133705 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #set $matrices = [] - #set $mlabels = [] - #for $counter, $i in enumerate($input_files): - ln -s $i.matrix #echo str($counter)+'_matrix'#; - #silent $matrices.append( '%s_matrix' % $counter ) - - #if str($i.mlabel.value) != "": - #set $mlabels += ['"%s"' % ($i.mlabel.value)] - #else - #set $mlabels += ['"%s"' % ($i.matrix.name)] - #end if - #end for - #set $mlabels = ' '.join($mlabels) - #set $matrices = ' '.join($matrices) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': - #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': - #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: - --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans - #end if - #end if - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -.. class:: infomark - -For more information on the tools, please visit our `help site`_. - -If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com - -This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. - -.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ -.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de -.. _help site: https://hicexplorer.readthedocs.org - - - - - - - - - - - - - - - - - - - - - - - - #import tempfile - #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) - #set files=[] - #set labels=[] - #for $i in $input_files: - #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) - #set $temp_input_path = $temp_input_handle.name - #silent $temp_input_handle.close() - #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) - #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) - #silent $files.append('%s.bam' % $temp_input_path) - - ##set $files += [str($i.bamfile)] - #if str($i.label.value) != "": - #set $labels += ["\"%s\"" % ($i.label.value)] - #else - #set $labels += ["\"%s\"" % ($i.bamfile.name)] - #end if - #end for - - - - #import tempfile - #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) - #set files=[] - #set labels=[] - #for $i in $input_files: - #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) - #set $temp_input_path = $temp_input_handle.name - #silent $temp_input_handle.close() - #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) - #silent $files.append('%s.bw' % $temp_input_path) - - ##set $files += [str($i.bigwigfile)] - #if str($i.label.value) != "": - #set $labels += ["\"%s\"" % ($i.label.value)] - #else - #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] - #end if - #end for - - - - - - - - - - - - - - - - - - - - - - - - #if $source.ref_source=="history": - --genome $source.input1 - #else: - --genome "${source.input1_2bit.fields.path}" - #end if - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - (( - output['showOutputSettings'] == 'yes' and - output['saveMatrix'] is True - )) - - - - - - - - (( - output['showOutputSettings'] == 'yes' and - output['saveData'] is True - )) - - - - - (( - output['showOutputSettings'] == 'yes' and - output['saveSortedRegions'] is True - )) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r 43332e51a712 -r b05f292d220c static/images/hicAggregateContacts.png Binary file static/images/hicAggregateContacts.png 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