{ "report_data_sources": { "RSeQC": { "infer_experiment": { "G175_M3_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M3/Read_Strandness/G175_M3_Read_Strandness.txt", "G175_M12_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M12/Read_Strandness/G175_M12_Read_Strandness.txt", "G175_M13_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M13/Read_Strandness/G175_M13_Read_Strandness.txt", "G175_M8_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M8/Read_Strandness/G175_M8_Read_Strandness.txt", "G175_M4_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M4/Read_Strandness/G175_M4_Read_Strandness.txt", "G175_M1_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M1/Read_Strandness/G175_M1_Read_Strandness.txt", "G175_M11_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M11/Read_Strandness/G175_M11_Read_Strandness.txt", "G175_M9_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M9/Read_Strandness/G175_M9_Read_Strandness.txt", "G175_M6_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M6/Read_Strandness/G175_M6_Read_Strandness.txt", "G175_M5_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M5/Read_Strandness/G175_M5_Read_Strandness.txt", "G175_M2_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M2/Read_Strandness/G175_M2_Read_Strandness.txt", "G175_M10_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M10/Read_Strandness/G175_M10_Read_Strandness.txt", "G175_M7_Read_Strandness": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M7/Read_Strandness/G175_M7_Read_Strandness.txt" } }, "featureCounts": { "all_sections": { "G175_M3_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M3/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G175_M3_featureCounts.out.summary", 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"/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M9/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G175_M9_featureCounts.out.summary", "G175_M6_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M6/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G175_M6_featureCounts.out.summary", "G175_M5_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M5/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G175_M5_featureCounts.out.summary", "G175_M2_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M2/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G175_M2_featureCounts.out.summary", "G175_M10_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M10/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G175_M10_featureCounts.out.summary", "G175_M7_sorted": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M7/featureCounts/RefSeqLncRNA76k_FullGeneBody_GTF/G175_M7_featureCounts.out.summary" } }, "Samtools": { "flagstat": { 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"G175_M13_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M13/aligner/G175_M13_statistics_for_all_accepted_reads.txt", "G175_M13_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M13/aligner/G175_M13_statistics_for_primary_reads.txt", "G175_M13_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M13/aligner/G175_M13_statistics_for_primary_unique_reads.txt", "G175_M8_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M8/aligner/G175_M8_statistics_for_primary_unique_reads.txt", "G175_M8_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M8/aligner/G175_M8_statistics_for_all_accepted_reads.txt", "G175_M8_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M8/aligner/G175_M8_statistics_for_primary_reads.txt", "G175_M4_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M4/aligner/G175_M4_statistics_for_primary_reads.txt", "G175_M4_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M4/aligner/G175_M4_statistics_for_all_accepted_reads.txt", "G175_M4_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M4/aligner/G175_M4_statistics_for_primary_unique_reads.txt", "G175_M1_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M1/aligner/G175_M1_statistics_for_all_accepted_reads.txt", "G175_M1_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M1/aligner/G175_M1_statistics_for_primary_unique_reads.txt", "G175_M1_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M1/aligner/G175_M1_statistics_for_primary_reads.txt", "G175_M11_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M11/aligner/G175_M11_statistics_for_primary_unique_reads.txt", "G175_M11_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M11/aligner/G175_M11_statistics_for_primary_reads.txt", "G175_M11_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M11/aligner/G175_M11_statistics_for_all_accepted_reads.txt", "G175_M9_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M9/aligner/G175_M9_statistics_for_primary_unique_reads.txt", "G175_M9_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M9/aligner/G175_M9_statistics_for_all_accepted_reads.txt", "G175_M9_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M9/aligner/G175_M9_statistics_for_primary_reads.txt", "G175_M6_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M6/aligner/G175_M6_statistics_for_primary_unique_reads.txt", "G175_M6_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M6/aligner/G175_M6_statistics_for_primary_reads.txt", "G175_M6_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M6/aligner/G175_M6_statistics_for_all_accepted_reads.txt", "G175_M5_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M5/aligner/G175_M5_statistics_for_all_accepted_reads.txt", "G175_M5_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M5/aligner/G175_M5_statistics_for_primary_unique_reads.txt", "G175_M5_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M5/aligner/G175_M5_statistics_for_primary_reads.txt", "G175_M2_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M2/aligner/G175_M2_statistics_for_all_accepted_reads.txt", "G175_M2_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M2/aligner/G175_M2_statistics_for_primary_reads.txt", "G175_M2_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M2/aligner/G175_M2_statistics_for_primary_unique_reads.txt", "G175_M10_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M10/aligner/G175_M10_statistics_for_primary_unique_reads.txt", "G175_M10_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M10/aligner/G175_M10_statistics_for_primary_reads.txt", "G175_M10_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M10/aligner/G175_M10_statistics_for_all_accepted_reads.txt", "G175_M7_statistics_for_primary_unique_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M7/aligner/G175_M7_statistics_for_primary_unique_reads.txt", "G175_M7_statistics_for_all_accepted_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M7/aligner/G175_M7_statistics_for_all_accepted_reads.txt", "G175_M7_statistics_for_primary_reads": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M7/aligner/G175_M7_statistics_for_primary_reads.txt" } }, "STAR": { "SummaryLog": { "G175_M3_G175_M3": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M3/aligner/G175_M3_G175_M3_Log.final.out", "G175_M12_G175_M12": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M12/aligner/G175_M12_G175_M12_Log.final.out", "G175_M13_G175_M13": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M13/aligner/G175_M13_G175_M13_Log.final.out", "G175_M8_G175_M8": "/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M8/aligner/G175_M8_G175_M8_Log.final.out", "G175_M4_G175_M4": 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"/projectnb/wax-dk/max/G174_G178_2024/G175/SAMPLES/G175_M7/aligner/G175_M7_G175_M7_Log.final.out" } } }, "report_general_stats_data": [ { "G175_M3_sorted": { "Total": 19411632, "Assigned": 18240765, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 1170867, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 93.96821967364723 }, "G175_M12_sorted": { "Total": 15370003, "Assigned": 14617980, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 752023, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.10720329722773 }, "G175_M13_sorted": { "Total": 10281868, "Assigned": 9757463, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 524405, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 94.89971083075565 }, "G175_M8_sorted": { "Total": 14636544, "Assigned": 14003809, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 632735, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.67701911052227 }, "G175_M4_sorted": { "Total": 15500490, "Assigned": 14793024, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 707466, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.43584751191736 }, "G175_M1_sorted": { "Total": 15067465, "Assigned": 14290577, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 776888, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 94.8439369197141 }, "G175_M11_sorted": { "Total": 12296359, "Assigned": 11703192, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 593167, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.17607610512998 }, "G175_M9_sorted": { "Total": 13999790, "Assigned": 13361862, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 637928, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.44330307811761 }, "G175_M6_sorted": { "Total": 13952916, "Assigned": 13302736, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 650180, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.34018552107673 }, "G175_M5_sorted": { "Total": 13989816, "Assigned": 13266700, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 723116, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 94.83112572745775 }, "G175_M2_sorted": { "Total": 13757981, "Assigned": 13068999, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 688982, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 94.99212856886487 }, "G175_M10_sorted": { "Total": 13200806, "Assigned": 12655552, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, "Unassigned_NoFeatures": 545254, "Unassigned_Unmapped": 0, "Unassigned_MappingQuality": 0, "Unassigned_FragmentLength": 0, "Unassigned_Chimera": 0, "Unassigned_Secondary": 0, "Unassigned_Nonjunction": 0, "Unassigned_Duplicate": 0, "percent_assigned": 95.86954008717346 }, "G175_M7_sorted": { "Total": 14752215, "Assigned": 14138178, "Unassigned_Ambiguity": 0, "Unassigned_MultiMapping": 0, 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"G175_M7_sorted", "G175_M8_sorted", "G175_M9_sorted" ] ], "datasets": [ [ { "name": "Assigned", "data": [ 12655552.0, 11703192.0, 14617980.0, 9757463.0, 14290577.0, 13068999.0, 18240765.0, 14793024.0, 13266700.0, 13302736.0, 14138178.0, 14003809.0, 13361862.0 ] }, { "name": "Unassigned: No Features", "data": [ 545254.0, 593167.0, 752023.0, 524405.0, 776888.0, 688982.0, 1170867.0, 707466.0, 723116.0, 650180.0, 614037.0, 632735.0, 637928.0 ] } ] ], "config": { "id": "featureCounts_assignment_plot", "title": "featureCounts: Assignments", "ylab": "# Reads", "cpswitch_counts_label": "Number of Reads" } }, "samtools-flagstat-dp": { "plot_type": "beeswarm", "samples": [ [ "G175_M3_statistics_for_primary_unique_reads", "G175_M3_statistics_for_primary_reads", "G175_M3_statistics_for_all_accepted_reads", "G175_M12_statistics_for_all_accepted_reads", "G175_M12_statistics_for_primary_unique_reads", "G175_M12_statistics_for_primary_reads", "G175_M13_statistics_for_all_accepted_reads", 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