# HG changeset patch
# User iuc
# Date 1524814556 14400
# Node ID 495ae38f6e0d220a75ad83ebb8bc6a13ed293eda
# Parent 707f691c974c86755355e9e0af7764720a9d97d9
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit eec0a4d5a7c5ba4ec0fbd2ead8280c3d143bb9d8
diff -r 707f691c974c -r 495ae38f6e0d hicBuildMatrix.xml
--- a/hicBuildMatrix.xml Wed Mar 07 03:42:32 2018 -0500
+++ b/hicBuildMatrix.xml Fri Apr 27 03:35:56 2018 -0400
@@ -1,5 +1,5 @@
- creates a contact matrix
+ create a contact matrix
hicBuildMatrix
macros.xml
@@ -38,8 +38,10 @@
#end if
--outFileName matrix.$outputFormat
-
- --outBam ./unsorted.bam
+
+ #if $outBam_Boolean:
+ $outBam_Boolean ./unsorted.bam
+ #end if
$keepSelfCircles
@@ -52,7 +54,7 @@
#end if
--threads @THREADS@
-
+
--QCfolder ./QCfolder
&&
mv ./QCfolder/* $qc.files_path/
@@ -60,13 +62,16 @@
mv $qc.files_path/hicQC.html $qc
&& mv $qc.files_path/*.log raw_qc
&& mv matrix.$outputFormat matrix
- && samtools sort ./unsorted.bam -o sorted.bam
-
+ #if $outBam_Boolean:
+ && samtools sort ./unsorted.bam -o sorted.bam
+ #end if
+
]]>
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Creation of the contact matrix
===============================
-``hicBuildMatrix`` creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files
-corresponding to the first and second mates of the paired-end H-C reads. The sam and bam files should
-not be sorted by position. There are two main options to create the Hi-C contact matrix, either by
-fixed bin size (eg. 10.000 bp) or by bins of variable restriction fragment size length.
-``hicBuildMatrix`` generates a quality control output that can be used to analyze the quality of the Hi-C reads.
-Input
+**hicBuildMatrix** creates a contact matrix based on Hi-C read pairs. It requires two sam or bam files
+corresponding to the first and second mates of the paired-end Hi-C reads mapped on the reference genome.
+The sam and bam files should not be sorted by position. There are two main options to create the Hi-C contact matrix,
+either by fixed bin size (eg. 10000 bp) or by bins of variable length following restriction enzyme sites location in the genome (restriction enzyme resolution).
+**hicBuildMatrix** generates a quality control output that can be used to analyze the quality of the Hi-C reads to assess if the experiment and sequencing were successful.
+
+_________________
+
+
+Usage
-----
-`hicBuildMatrix` is having the following parameters:
-
-Parameters
-__________
-
-- two input BAM/SAM files
-- a bin size
-- a restriction cut file as an alternative to the bin size
-- restriction sequence: e.g. HindIII: GATC
+This tool must be used on paired sam / bam files produced with a program that supports local alignment (e.g. Bowtie2) where both PE reads are mapped using the --local option.
+_________________
Output
------
-`hicBuildMatrix` creates as an output:
- - the contact matrix
- - a bam file with the accepted alignments
- - a quality report.
+**hicBuildMatrix** creates multiple outputs:
+
+ - The contact matrix used by HiCExplorer for all downstream analyses.
+ - A bam file with the accepted alignments, which can be useful to inspect the distribution of valid Hi-C reads pairs, notably around restriction enzyme sites or for other downstream analyses. This file is not used by any HiCExplorer tools.
+ - A quality control report to assess if the Hi-C protocol and library contrusction were successful.
Example plot
------------------------------------------------------------------
-.. image:: $PATH_TO_IMAGES/SRR027956.svg
- :width: 70%
+++++++++++++
+
+.. image:: hicPlotMatrix.png
+ :width: 50%
-Contact matrix created with `hicPlotMatrix`.
+Contact matrix of *Drosophila melanogaster* embryos built with **hicBuildMatrix** and visualized using ``hicPlotMatrix``. Hi-C matrix bins were merged to a 25 kb bin size before plotting using ``hicMergeMatrixBins``.
+
+
+
Quality report
---------------
-
-The quality report gives you information about:
-
-- how many pairs were used to build the contact matrix
-- dangling end pairs: These are reads that start with the restriction site and constitute reads that were digested but no ligated.
-- same fragment pairs: These are read mates, facing inward, separated by up to 800 bp that do not have a restriction enzyme in between. These read pairs are not valid Hi-C pairs.
-- self circles: Self circles are defined as pairs within 25kb with 'outward' read orientation
-- self ligations: These are read pairs with a restriction site in between that are within 800 bp.
+++++++++++++++
-Contact distance:
-_________________
-- inter chromosomal
-- short range < 20 kb
-- long range
-
-Read orientation:
-_________________
-- inward pairs
-- outward pairs
-- left pairs
-- right pairs
+A quality report is produced alongside the contact matrix.
.. image:: $PATH_TO_IMAGES/hicQC.png
- :width: 70 %
+ :width: 40%
+
+Several plots, that are described in details below, are comprised inside this report.
+
+.. image:: $PATH_TO_IMAGES/hicQC_pairs_sequenced.png
+ :width: 40%
+
+On the plot above, we can see how many reads were sequenced per sample (pairs considered), how many reads were mappable, unique and of high quality and how many reads passed all quality controls and are thus useful for further analysis (pairs used). All quality controls used for read filtering are explained below.
+
+.. image:: $PATH_TO_IMAGES/hicQC_unmappable_and_non_unique.png
+ :width: 40%
+
+The figure above contains the fraction of reads with respect to the total number of reads that did not map, that have a low quality score or that didn't map uniquely to the genome. In our example we can see that Sample 3 has the highest fraction of pairs used. We explain the differences between the three samples on the plot below.
+
+.. image:: $PATH_TO_IMAGES/hicQC_pairs_discarded.png
+ :width: 40%
+
+This figure contains the fraction of read pairs (with respect to mappable and unique reads) that were discarded when building the Hi-C matrix. You can find the description of each category below:
+
+ - **Dangling ends:** reads that start with the restriction site and constitute reads that were digested but not ligated. Sample 1 in our example has a high fraction of dangling ends (and thus a low proportion of pairs used). Reasons for this can be inefficient ligation or insufficient removal of danging ends during samples preparation.
+ - **Duplicated pairs:** reads that have the same sequence due to PCR amplification. For example, Sample 2 was amplified too much and thus has a very high fraction of duplicated pairs.
+
+ - **Same fragment:** read mates facing inward, separated by up to 800bp that do not have a restriction enzyme site in between. These read pairs are not valid Hi-C pairs and are thus discarded from further analyses.
+
+ - **Self circle:** read pairs within 25kb with 'outward' read orientation.
+
+ - **Self ligation:** read pairs with a restriction site in between that are within 800bp.
+
+.. image:: $PATH_TO_IMAGES/hicQC_distance.png
+ :width: 40%
+
+The figure above contains the fraction of read pairs (with respect to mappable reads) that compose inter chromosomal, short range (< 20kb) or long range contacts. Inter chromosomal reads of a wild-type sample are expected to be low. Trans-chromosomal contacts can be primarily considered as random ligation events. These would be expected to contribute to technical noise that may obscure some of the finer features in the Hi-C datasets (Nagano *et al.* 2015, Comparison of Hi-C results using in-solution versus in-nucleus ligation, doi: https://doi.org/10.1186/s13059-015-0753-7). As such, a high fraction of inter chromosomal reads is an indicator of low sample quality, but it can also be associated to cell cycle changes (Nagano *et al.* 2018, Cell-cycle dynamics of chromosomal organisation at single-cell resolution, doi: https://doi.org/10.1038/nature23001).
+
+Short range and long range contacts proportions can be associated to how the fixation is performed during Hi-C sample preparation. These two proportions also directly impact the Hi-C corrected counts versus genomic distance plots generated by hicPlotDistVsCounts.
+
+.. image:: $PATH_TO_IMAGES/hicQC_read_orientation.png
+ :width: 40%
+
+The last figure shows the fractions of inward, outward, left or right read pairs (with respect to mappable reads). Deviations from an equal distribution indicates problems during sample preparation.
+
+_________________
| For more information about HiCExplorer please consider our documentation on readthedocs.io_.
.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
-
-
]]>
diff -r 707f691c974c -r 495ae38f6e0d involucro
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diff -r 707f691c974c -r 495ae38f6e0d macros.xml
--- a/macros.xml Wed Mar 07 03:42:32 2018 -0500
+++ b/macros.xml Fri Apr 27 03:35:56 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
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- \${GALAXY_SLOTS:-4}
-<<<<<<< HEAD
- 2.0
-
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- #if $use_range.select_use_range == "yes_use_range":
- --range $range_min:$range_max
- #end if
-
-
-=======
- 2.1alpha1
->>>>>>> joachimwolff-master
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- hicexplorer
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- @BINARY@ --version
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- #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)
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- #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
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-.. class:: infomark
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-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
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- #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
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- #set $temp_dir = os.path.abspath(tempfile.mkdtemp())
- #set files=[]
- #set labels=[]
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- #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
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- --genome $source.input1
- #else:
- --genome "${source.input1_2bit.fields.path}"
- #end if
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- output['showOutputSettings'] == 'yes' and
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diff -r 707f691c974c -r 495ae38f6e0d static/images/hicAggregateContacts.png
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diff -r 707f691c974c -r 495ae38f6e0d test-data/compare_matrices_log2ratio.h5
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diff -r 707f691c974c -r 495ae38f6e0d test-data/multiFDR_zscore_matrix.h5
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diff -r 707f691c974c -r 495ae38f6e0d test-data/small_matrix_50kb_pearson_pca1_plot.svg
--- a/test-data/small_matrix_50kb_pearson_pca1_plot.svg Wed Mar 07 03:42:32 2018 -0500
+++ b/test-data/small_matrix_50kb_pearson_pca1_plot.svg Fri Apr 27 03:35:56 2018 -0400
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