| Previous changeset 2:cab616fe7e64 (2024-11-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 69bb60ab875c1c1769298678f0890d8b92f1899d |
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modified:
macros.xml test-data/cHi-C/chicExportData/aggregate.tar.gz test-data/cHi-C/chicQualityControl/histogram.png test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report test-data/cHi-C/chicQualityControl/sparsity.png test-data/cHi-C/plots.tar.gz test-data/hicAggregateContacts_results1.png test-data/hicAverageRegions/result_rangeInBins_100.npz test-data/hicAverageRegions/result_range_100000.npz test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png test-data/hicCompartmentsPolarization/output_matrix.npz test-data/hicConvertFormat/small_test_matrix_chr4.homer test-data/hicCorrectMatrix/diagnostic_plot.png test-data/hicCorrelate_heatmap_result1.png test-data/hicCorrelate_scatter_result1.png test-data/hicDetectLoops/loops.bedgraph test-data/hicDifferentialTAD/accepted.txt test-data/hicDifferentialTAD/rejected.txt test-data/hicHyperoptDetectLoops/loops.bedgraph test-data/hicInfo/hicInfo_output.txt test-data/hicInterIntraTAD/output.txt test-data/hicInterIntraTAD/plot.png test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf test-data/hicPCA/pca1_test1.bw test-data/hicPCA/pca2_test1.bw test-data/hicPlotAverageRegions/defaults.png test-data/hicPlotAverageRegions/defaults_log.png test-data/hicPlotAverageRegions/defaults_log1p.png test-data/hicPlotAverageRegions/defaults_log_vmin_vmax.png test-data/hicPlotDistVsCounts_result1.png test-data/hicPlotDistVsCounts_result2.png test-data/hicPlotMatrix/plot1.png test-data/hicPlotMatrix/plot2.pdf test-data/hicPlotMatrix/plot3_pca.svg test-data/hicPlotSVL/p_values.txt test-data/hicPlotSVL/plot.png test-data/hicPlotSVL/ratios.txt test-data/hicQuickQC/QC.log test-data/hicValidateLocations/overlap_smc3_statistics test-data/li_viewpoint_32-33Mb.png test-data/li_viewpoint_32Mb.png test-data/small_test_matrix_result_sorted.bam |
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added:
test-data/raw_qc_report_micro-c test-data/small_test_matrix_result_sorted_microc.bam |
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| diff -r cab616fe7e64 -r 1a31e75e979e macros.xml --- a/macros.xml Mon Nov 04 23:50:05 2024 +0000 +++ b/macros.xml Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@TOOL_VERSION@">3.7.5</token> + <token name="@TOOL_VERSION@">3.7.6</token> <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">23.0</token> <token name="@USE_RANGE@"> |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/cHi-C/chicExportData/aggregate.tar.gz |
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| Binary file test-data/cHi-C/chicExportData/aggregate.tar.gz has changed |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/cHi-C/chicQualityControl/histogram.png |
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| Binary file test-data/cHi-C/chicQualityControl/histogram.png has changed |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter --- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,4 +1,4 @@ -# Created with chicQualityControl version 3.7.5 +# Created with chicQualityControl version 3.7.6 # A sparsity of -1.0 indicates a faulty reference point e.g. no data for this reference point was in the matrix. # Used Matrices 0_matrix.cool 1_matrix.cool # Chromosome Start End Sparsity 0_matrix.cool Sparsity 1_matrix.cool |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report --- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,4 +1,4 @@ -# Created with chicQualityControl version 3.7.5 +# Created with chicQualityControl version 3.7.6 # QC report for matrices: 0_matrix.cool 1_matrix.cool #Sparsity threshold for rejection: sparsity <= 0.05 are rejected. |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/cHi-C/chicQualityControl/sparsity.png |
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| Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/cHi-C/plots.tar.gz |
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| Binary file test-data/cHi-C/plots.tar.gz has changed |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicAggregateContacts_results1.png |
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| Binary file test-data/hicAggregateContacts_results1.png has changed |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicAverageRegions/result_rangeInBins_100.npz |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicAverageRegions/result_range_100000.npz |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicCompartmentsPolarization/compartmentsPolarizationRatio.png |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicCompartmentsPolarization/output_matrix.npz |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicConvertFormat/small_test_matrix_chr4.homer |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicCorrectMatrix/diagnostic_plot.png |
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| Binary file test-data/hicCorrectMatrix/diagnostic_plot.png has changed |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicCorrelate_heatmap_result1.png |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicCorrelate_scatter_result1.png |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicDetectLoops/loops.bedgraph --- a/test-data/hicDetectLoops/loops.bedgraph Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicDetectLoops/loops.bedgraph Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -0,0 +1,2 @@ +chr3L 640000 645000 chr3L 645000 650000 0.10258046718611576 +chr2L 18670000 18675000 chr2L 18675000 18680000 0.23000508888575644 |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicDifferentialTAD/accepted.txt --- a/test-data/hicDifferentialTAD/accepted.txt Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicDifferentialTAD/accepted.txt Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.7.5 +# Created with HiCExplorer's hicDifferentialTAD version 3.7.6 # H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential. # Accepted regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one # Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicDifferentialTAD/rejected.txt --- a/test-data/hicDifferentialTAD/rejected.txt Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicDifferentialTAD/rejected.txt Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicDifferentialTAD version 3.7.5 +# Created with HiCExplorer's hicDifferentialTAD version 3.7.6 # H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential. # Rejected regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one # Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicHyperoptDetectLoops/loops.bedgraph --- a/test-data/hicHyperoptDetectLoops/loops.bedgraph Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicHyperoptDetectLoops/loops.bedgraph Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,3 +1,3 @@ -# Created by HiCExplorer hicHyperoptDetectLoops 3.7.3 +# Created by HiCExplorer hicHyperoptDetectLoops 3.7.6 -{'chrPrefixLoops': None, 'matrixFile': 'matrix.cool', 'maxLoopDistance': 2300000, 'maximumNumberOfLoops': 5, 'oet': 1.230889168935347, 'p': 0.048940366161874596, 'peakWidth': 6, 'pit': 22.88867979095296, 'pp': 0.13365961880597724, 'proteinFile': '/tmp/tmpjkr0wi60/files/6/a/7/dataset_6a78c4eb-7f74-459b-9ed8-08972cc0c5f4.dat', 'resolution': 2, 'threads': 1, 'windowSize': 6} \ No newline at end of file +{'chrPrefixLoops': None, 'matrixFile': 'matrix.cool', 'maxLoopDistance': 1300000, 'maximumNumberOfLoops': 5, 'oet': 2.8714859798937415, 'p': 0.012586549394837264, 'peakWidth': 8, 'pit': 63.88073951584609, 'pp': 0.06112040451977812, 'proteinFile': '/tmp/tmpgf9pvov_/files/2/9/7/dataset_2978768e-39c0-4648-aa6e-8f81c54806cb.dat', 'resolution': 2, 'threads': 1, 'windowSize': 11} \ No newline at end of file |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicInfo/hicInfo_output.txt --- a/test-data/hicInfo/hicInfo_output.txt Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicInfo/hicInfo_output.txt Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,4 +1,4 @@ -# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.5 +# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.6 File: matrix_name.h5 Size: 33,754 Bin_length: 5000 |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicInterIntraTAD/output.txt --- a/test-data/hicInterIntraTAD/output.txt Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicInterIntraTAD/output.txt Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicInterIntraTAD version 3.7.5 +# Created with HiCExplorer's hicInterIntraTAD version 3.7.6 # Chromosome start end name score strand inter_left_sum inter_right_sum inter_left_density inter_right_density inter_left_number_of_contacts inter_right_number_of_contacts inter_left_number_of_contacts_nnz inter_right_number_of_contacts_nnz intra_sum intra_number_of_contacts intra_number_of_contacts_nnz intra_density inter_left_intra_ratio inter_right_intra_ratio inter_left_inter_right_intra_ratio chr2 17100000 18100000 ID_0.01_10 -0.230354 . 0 148.64979 0 1.0 0 90 0 90 289.00809 100 100 1.0 0.0 0.5143447368549441 0.5143447368549441 chr2 18100000 19100000 ID_0.01_11 -0.5135365 . 162.11248 211.04027000000002 1.0 1.0 100 140 100 140 277.9356 100 100 1.0 0.5832735353081793 0.7593135604075189 1.3425870957156982 |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicInterIntraTAD/plot.png |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicMergeDomains/ctcf_plot/two_files_plot_1.pdf |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicPlotDistVsCounts_result2.png |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicPlotMatrix/plot1.png |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicPlotMatrix/plot2.pdf |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicPlotMatrix/plot3_pca.svg --- a/test-data/hicPlotMatrix/plot3_pca.svg Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicPlotMatrix/plot3_pca.svg Thu Dec 05 18:31:59 2024 +0000 |
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| b'@@ -6,11 +6,11 @@\n <rdf:RDF xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://creativecommons.org/ns#" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n <cc:Work>\n <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>\n- <dc:date>2024-02-11T14:04:07.014551</dc:date>\n+ <dc:date>2024-12-02T19:04:38.605351</dc:date>\n <dc:format>image/svg+xml</dc:format>\n <dc:creator>\n <cc:Agent>\n- <dc:title>Matplotlib v3.6.2, https://matplotlib.org/</dc:title>\n+ <dc:title>Matplotlib v3.8.4, https://matplotlib.org/</dc:title>\n </cc:Agent>\n </dc:creator>\n </cc:Work>\n@@ -38,17 +38,17 @@\n " style="fill: #ffffff"/>\n </g>\n <image xlink:href="data:image/png;base64,\n-iVBORw0KGgoAAAANSUhEUgAAAD8AAAA5CAYAAACBBvPCAAABNUlEQVR4nO2ZwRKDIAxEo9f2E+3f9RO92xOO7aAlkBBi9h0ddVzZXQSnB9FGQZmtH8ASiI8KxN+FdeEdn9D2QYH4qNxKfK7YzsqOCIXnm3WrHzv34uk1VV/q0vYpx893231cipfCne3X5brBOWDkowLxmnDzmc6XyvUVLPE1Qo7TUcn16fzWaawEFF5UsuJL7a2Vy3/3VZ3nf7N6V7IjLyG8tuV7Upx5zsPVOMfCaWj7qKiKt8gxB9h+VLSdg5HvwYj5VxG/L0sP28rc1d3VeVIvUkX8LrRhW/nrPoXHucxE/S05yroBhRcVMfGt0bGYDWD7qEC8dt5G/LojEsq81z2/3fYto6MlHKs6RVB4Z4xaVFJgD8/6IaxA5o9w/8zUMEocWLb3+jFzBsv2SXivX8jahC68DyTZYHVMEGd/AAAAAElFTkSuQmCC" id="imagee9b55c69ef" transform="scale(1 -1) translate(0 -410.4)" x="72" y="-36" width="453.6" height="410.4"/>\n+iVBORw0KGgoAAAANSUhEUgAAAD8AAAA5CAYAAACBBvPCAAABNUlEQVR4nO2ZwRKDIAxEo9f2E+3f9RO92xOO7aAlkBBi9h0ddVzZXQSnB9FGQZmtH8ASiI8KxN+FdeEdn9D2QYH4qNxKfK7YzsqOCIXnm3WrHzv34uk1VV/q0vYpx893231cipfCne3X5brBOWDkowLxmnDzmc6XyvUVLPE1Qo7TUcn16fzWaawEFF5UsuJL7a2Vy3/3VZ3nf7N6V7IjLyG8tuV7Upx5zsPVOMfCaWj7qKiKt8gxB9h+VLSdg5HvwYj5VxG/L0sP28rc1d3VeVIvUkX8LrRhW/nrPoXHucxE/S05yroBhRcVMfGt0bGYDWD7qEC8dt5G/LojEsq81z2/3fYto6MlHKs6RVB4Z4xaVFJgD8/6IaxA5o9w/8zUMEocWLb3+jFzBsv2SXivX8jahC68DyTZYHVMEGd/AAAAAElFTkSuQmCC" id="image807d780cbb" transform="scale(1 -1) translate(0 -410.4)" x="72" y="-36" width="453.6" height="410.4"/>\n <g id="matplotlib.axis_1">\n <g id="xtick_1">\n <g id="line2d_1">\n <defs>\n- <path id="m2f4bd1209e" d="M 0 0 \n+ <path id="m8489abdf3d" d="M 0 0 \n L 0 -3.5 \n " style="stroke: #000000; 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| b |
| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicPlotSVL/p_values.txt --- a/test-data/hicPlotSVL/p_values.txt Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicPlotSVL/p_values.txt Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicPlotSVL 3.7.5 +# Created with HiCExplorer's hicPlotSVL 3.7.6 # Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum # Short range contacts: <= 2000000 0_small_test_matrix.h5 1_small_test_matrix.h5 1.0 |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicPlotSVL/plot.png |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicPlotSVL/ratios.txt --- a/test-data/hicPlotSVL/ratios.txt Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicPlotSVL/ratios.txt Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,4 +1,4 @@ -# Created with HiCExplorer's hicPlotSVL 3.7.5 +# Created with HiCExplorer's hicPlotSVL 3.7.6 # Short range vs long range contacts per chromosome: raw data # Short range contacts: <= 2000000 # 0_small_test_matrix.h5 1_small_test_matrix.h5 |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicQuickQC/QC.log --- a/test-data/hicQuickQC/QC.log Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicQuickQC/QC.log Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,5 +1,5 @@ -File /tmp/tmpjkr0wi60/tmp/tmp8o_td4fd.h5 +File /tmp/tmpgf9pvov_/tmp/tmpovrpxt57.h5 Sequenced reads 983 Min rest. site distance 300 Max library insert size 1000 |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/hicValidateLocations/overlap_smc3_statistics --- a/test-data/hicValidateLocations/overlap_smc3_statistics Mon Nov 04 23:50:05 2024 +0000 +++ b/test-data/hicValidateLocations/overlap_smc3_statistics Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -1,5 +1,5 @@ -# HiCExplorer hicValidateLocations 3.7.5 -# Overlap of loop file /tmp/tmpjkr0wi60/files/a/f/1/dataset_af1f91e3-b1bd-4c1c-8842-935caae86bf2.dat with protein file /tmp/tmpjkr0wi60/files/e/6/e/dataset_e6e4503d-c6a1-4370-bc34-70b2fae3fc95.dat +# HiCExplorer hicValidateLocations 3.7.6 +# Overlap of loop file /tmp/tmpgf9pvov_/files/2/9/c/dataset_29c1b4d3-8569-4405-ac40-08d8d9077d0d.dat with protein file /tmp/tmpgf9pvov_/files/4/8/3/dataset_48318067-0b54-463f-a9a7-9c751f3b7d1a.dat # Protein peaks: 3097 Matched Loops: 530 |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/li_viewpoint_32-33Mb.png |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/li_viewpoint_32Mb.png |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/raw_qc_report_micro-c --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw_qc_report_micro-c Thu Dec 05 18:31:59 2024 +0000 |
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| @@ -0,0 +1,24 @@ + +File matrix.cool +Sequenced reads 983 +Max library insert size 1000 + +# count (percentage w.r.t. total sequenced reads) +Pairs mappable, unique and high quality 300 (30.52) +Hi-C contacts 215 (21.87) +One mate unmapped 506 (51.48) +One mate not unique 13 (1.32) +Low mapping quality 164 (16.68) + +# count (percentage w.r.t. mappable, unique and high quality pairs) +same fragment 85 (28.33) +duplicated pairs 0 (0.00) + +# count (percentage w.r.t. total valid pairs used) +inter chromosomal 24 (11.16) +Intra short range (< 20kb) 61 (28.37) +Intra long range (>= 20kb) 130 (60.47) +Read pair type: inward pairs 42 (19.53) +Read pair type: outward pairs 66 (30.70) +Read pair type: left pairs 48 (22.33) +Read pair type: right pairs 35 (16.28) |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/small_test_matrix_result_sorted.bam |
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| diff -r cab616fe7e64 -r 1a31e75e979e test-data/small_test_matrix_result_sorted_microc.bam |
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