{ "report_data_sources": { "RSeQC": { "infer_experiment": { "G178_M9_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M9/Read_Strandness/G178_M9_Read_Strandness.txt", "G178_M10_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M10/Read_Strandness/G178_M10_Read_Strandness.txt", "G178_M12_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M12/Read_Strandness/G178_M12_Read_Strandness.txt", "G178_M11_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M11/Read_Strandness/G178_M11_Read_Strandness.txt", "G178_M13_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M13/Read_Strandness/G178_M13_Read_Strandness.txt", "G178_M5_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M5/Read_Strandness/G178_M5_Read_Strandness.txt", "G178_M1_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M1/Read_Strandness/G178_M1_Read_Strandness.txt", "G178_M6_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M6/Read_Strandness/G178_M6_Read_Strandness.txt", "G178_M2_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M2/Read_Strandness/G178_M2_Read_Strandness.txt", "G178_M7_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M7/Read_Strandness/G178_M7_Read_Strandness.txt", "G178_M3_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M3/Read_Strandness/G178_M3_Read_Strandness.txt", "G178_M8_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M8/Read_Strandness/G178_M8_Read_Strandness.txt", "G178_M4_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M4/Read_Strandness/G178_M4_Read_Strandness.txt" } }, "featureCounts": { "all_sections": { "G178_M9_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M9/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M9_featureCounts.out.summary", "G178_M10_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M10/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M10_featureCounts.out.summary", "G178_M12_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M12/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M12_featureCounts.out.summary", "G178_M11_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M11/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M11_featureCounts.out.summary", "G178_M13_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M13/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M13_featureCounts.out.summary", "G178_M5_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M5/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M5_featureCounts.out.summary", "G178_M1_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M1/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M1_featureCounts.out.summary", "G178_M6_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M6/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M6_featureCounts.out.summary", "G178_M2_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M2/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M2_featureCounts.out.summary", "G178_M7_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M7/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M7_featureCounts.out.summary", "G178_M3_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M3/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M3_featureCounts.out.summary", "G178_M8_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M8/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M8_featureCounts.out.summary", "G178_M4_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M4/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G178_M4_featureCounts.out.summary" } }, "Samtools": { "flagstat": { 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"/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M12/aligner/G178_M12_statistics_for_primary_reads.txt", "G178_M12_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M12/aligner/G178_M12_statistics_for_all_accepted_reads.txt", "G178_M12_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M12/aligner/G178_M12_statistics_for_primary_unique_reads.txt", "G178_M11_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M11/aligner/G178_M11_statistics_for_primary_reads.txt", "G178_M11_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M11/aligner/G178_M11_statistics_for_all_accepted_reads.txt", "G178_M11_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M11/aligner/G178_M11_statistics_for_primary_unique_reads.txt", "G178_M13_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M13/aligner/G178_M13_statistics_for_primary_reads.txt", "G178_M13_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M13/aligner/G178_M13_statistics_for_all_accepted_reads.txt", "G178_M13_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M13/aligner/G178_M13_statistics_for_primary_unique_reads.txt", "G178_M5_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M5/aligner/G178_M5_statistics_for_primary_reads.txt", "G178_M5_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M5/aligner/G178_M5_statistics_for_all_accepted_reads.txt", "G178_M5_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M5/aligner/G178_M5_statistics_for_primary_unique_reads.txt", "G178_M1_statistics_for_primary_reads": 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"/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M2/aligner/G178_M2_statistics_for_all_accepted_reads.txt", "G178_M2_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M2/aligner/G178_M2_statistics_for_primary_unique_reads.txt", "G178_M2_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M2/aligner/G178_M2_statistics_for_primary_reads.txt", "G178_M7_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M7/aligner/G178_M7_statistics_for_primary_reads.txt", "G178_M7_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M7/aligner/G178_M7_statistics_for_primary_unique_reads.txt", "G178_M7_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M7/aligner/G178_M7_statistics_for_all_accepted_reads.txt", "G178_M3_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M3/aligner/G178_M3_statistics_for_primary_unique_reads.txt", "G178_M3_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M3/aligner/G178_M3_statistics_for_primary_reads.txt", "G178_M3_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M3/aligner/G178_M3_statistics_for_all_accepted_reads.txt", "G178_M8_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M8/aligner/G178_M8_statistics_for_all_accepted_reads.txt", "G178_M8_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M8/aligner/G178_M8_statistics_for_primary_reads.txt", "G178_M8_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M8/aligner/G178_M8_statistics_for_primary_unique_reads.txt", "G178_M4_statistics_for_all_accepted_reads": 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"/projectnb/wax-dk/max/G174_G178_2024/G178/SAMPLES/G178_M4/aligner/G178_M4_G178_M4_Log.final.out" } } }, "report_general_stats_data": [ { "G178_M9_sorted": { "Total": 15405321, "Assigned": 13855952, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 1549369, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 89.94263735237973 }, "G178_M10_sorted": { "Total": 19449355, "Assigned": 16462989, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 2986366, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 84.64542397421405 }, "G178_M12_sorted": { "Total": 16487593, "Assigned": 14593022, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 1894571, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 88.50911106308847 }, "G178_M11_sorted": { "Total": 14902886, "Assigned": 13416629, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 1486257, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 90.0270524782918 }, "G178_M13_sorted": { "Total": 14683795, "Assigned": 12155037, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 2528758, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 82.77858006053613 }, "G178_M5_sorted": { "Total": 21563635, "Assigned": 18435455, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 3128180, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 85.49326215176616 }, "G178_M1_sorted": { "Total": 17287005, "Assigned": 14374522, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 2912483, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 83.15218281015132 }, "G178_M6_sorted": { "Total": 19376239, "Assigned": 17367437, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 2008802, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 89.6326526525607 }, "G178_M2_sorted": { "Total": 14363147, "Assigned": 12540923, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 1822224, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 87.31319814522541 }, "G178_M7_sorted": { "Total": 15366495, "Assigned": 13018752, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 2347743, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 84.72167530721873 }, "G178_M3_sorted": { "Total": 14772523, "Assigned": 13057384, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 1715139, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 88.38966776359055 }, "G178_M8_sorted": { "Total": 16815810, "Assigned": 15067054, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 1748756, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 89.60052474427339 }, "G178_M4_sorted": { "Total": 16491199, "Assigned": 13728979, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, 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"min": 0, "modify": 1e-06, "shared_key": "read_count", "placement": 101.0, "namespace": "Samtools", "rid": "mqc-generalstats-samtools-mapped_passed", "scale": "GnBu", "format": "{:,.1f}", "colour": "77,175,74", "hidden": null, "max": null, "ceiling": null, "floor": null, "minRange": null, "dmax": 48.43163, "dmin": 0.0 } }, { "uniquely_mapped_percent": { "title": "% Aligned", "description": "% Uniquely mapped reads", "max": 100, "min": 0, "suffix": "%", "scale": "YlGn", "namespace": "STAR", "rid": "mqc-generalstats-star-uniquely_mapped_percent", "format": "{:,.1f}", "colour": "152,78,163", "hidden": null, "ceiling": null, "floor": null, "minRange": null, "shared_key": null, "modify": null, "placement": 1000.0, "dmax": 100.0, "dmin": 0.0 }, "uniquely_mapped": { "title": "M Aligned", "description": "Uniquely mapped reads (millions)", "min": 0, "scale": "PuRd", "modify": 1e-06, "shared_key": "read_count", "namespace": "STAR", "rid": "mqc-generalstats-star-uniquely_mapped", "format": 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"datasets": [ [ { "name": "Sense", "data": [ 4.05, 3.0300000000000002, 3.54, 4.8, 3.44, 2.9000000000000004, 3.0300000000000002, 3.08, 4.24, 2.9000000000000004, 4.78, 2.96, 2.5100000000000002 ] }, { "name": "Antisense", "data": [ 93.85, 94.69, 94.39999999999999, 93.23, 94.78999999999999, 95.32000000000001, 95.19999999999999, 94.73, 94.11, 95.17999999999999, 93.0, 94.8, 95.48 ] }, { "name": "Undetermined", "data": [ 2.11, 2.2800000000000002, 2.06, 1.97, 1.78, 1.78, 1.76, 2.18, 1.6400000000000001, 1.92, 2.22, 2.2399999999999998, 2.01 ] } ] ], "config": { "id": "rseqc_infer_experiment_plot", "title": "RSeQC: Infer experiment", "ylab": "% Tags", "ymin": 0, "ymax": 100, "tt_percentages": false, "ylab_format": "{value}%", "cpswitch": false } }, "featureCounts_assignment_plot": { "plot_type": "bar_graph", "samples": [ [ "G178_M10_sorted", "G178_M11_sorted", "G178_M12_sorted", "G178_M13_sorted", "G178_M1_sorted", "G178_M2_sorted", "G178_M3_sorted", "G178_M4_sorted", "G178_M5_sorted", "G178_M6_sorted", "G178_M7_sorted", "G178_M8_sorted", "G178_M9_sorted" ] ], "datasets": [ [ { "name": "Assigned", "data": [ 16462989.0, 13416629.0, 14593022.0, 12155037.0, 14374522.0, 12540923.0, 13057384.0, 13728979.0, 18435455.0, 17367437.0, 13018752.0, 15067054.0, 13855952.0 ] }, { "name": "Unassigned: No Features", "data": [ 2986366.0, 1486257.0, 1894571.0, 2528758.0, 2912483.0, 1822224.0, 1715139.0, 2762220.0, 3128180.0, 2008802.0, 2347743.0, 1748756.0, 1549369.0 ] } ] ], "config": { "id": "featureCounts_assignment_plot", "title": "featureCounts: Assignments", "ylab": "# Reads", "cpswitch_counts_label": "Number of Reads" } }, "samtools-flagstat-dp": { "plot_type": "beeswarm", "samples": [ [ "G178_M9_statistics_for_primary_reads", "G178_M9_statistics_for_all_accepted_reads", "G178_M9_statistics_for_primary_unique_reads", "G178_M10_statistics_for_primary_unique_reads", "G178_M10_statistics_for_primary_reads", "G178_M10_statistics_for_all_accepted_reads", "G178_M12_statistics_for_primary_reads", "G178_M12_statistics_for_all_accepted_reads", "G178_M12_statistics_for_primary_unique_reads", "G178_M11_statistics_for_primary_reads", "G178_M11_statistics_for_all_accepted_reads", "G178_M11_statistics_for_primary_unique_reads", "G178_M13_statistics_for_primary_reads", "G178_M13_statistics_for_all_accepted_reads", "G178_M13_statistics_for_primary_unique_reads", "G178_M5_statistics_for_primary_reads", "G178_M5_statistics_for_all_accepted_reads", "G178_M5_statistics_for_primary_unique_reads", "G178_M1_statistics_for_primary_reads", "G178_M1_statistics_for_all_accepted_reads", "G178_M1_statistics_for_primary_unique_reads", "G178_M6_statistics_for_primary_reads", "G178_M6_statistics_for_all_accepted_reads", "G178_M6_statistics_for_primary_unique_reads", "G178_M2_statistics_for_all_accepted_reads", "G178_M2_statistics_for_primary_unique_reads", "G178_M2_statistics_for_primary_reads", "G178_M7_statistics_for_primary_reads", 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