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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-08-05, 22:21 based on data in:

        General Statistics

        Showing 325/325 rows and 5/6 columns.
        Sample NameM Reads Mapped% AssignedM Assigned% AlignedM Aligned
        G174REL_M10_G174REL_M10
        86.9%
        23.3
        G174REL_M10_sorted
        93.8%
        21.9
        G174REL_M10_statistics_for_all_accepted_reads
        58.5
        G174REL_M10_statistics_for_primary_reads
        50.6
        G174REL_M10_statistics_for_primary_unique_reads
        46.0
        G174REL_M11_G174REL_M11
        88.2%
        28.7
        G174REL_M11_sorted
        94.2%
        27.0
        G174REL_M11_statistics_for_all_accepted_reads
        71.3
        G174REL_M11_statistics_for_primary_reads
        62.1
        G174REL_M11_statistics_for_primary_unique_reads
        56.7
        G174REL_M12_G174REL_M12
        88.9%
        21.1
        G174REL_M12_sorted
        94.8%
        20.0
        G174REL_M12_statistics_for_all_accepted_reads
        52.4
        G174REL_M12_statistics_for_primary_reads
        45.5
        G174REL_M12_statistics_for_primary_unique_reads
        41.7
        G174REL_M13_G174REL_M13
        82.9%
        19.9
        G174REL_M13_sorted
        93.0%
        18.5
        G174REL_M13_statistics_for_all_accepted_reads
        52.7
        G174REL_M13_statistics_for_primary_reads
        44.0
        G174REL_M13_statistics_for_primary_unique_reads
        39.3
        G174REL_M1_G174REL_M1
        74.7%
        15.2
        G174REL_M1_sorted
        91.5%
        13.9
        G174REL_M1_statistics_for_all_accepted_reads
        45.6
        G174REL_M1_statistics_for_primary_reads
        34.7
        G174REL_M1_statistics_for_primary_unique_reads
        29.8
        G174REL_M2_G174REL_M2
        83.0%
        23.0
        G174REL_M2_sorted
        95.0%
        21.9
        G174REL_M2_statistics_for_all_accepted_reads
        58.1
        G174REL_M2_statistics_for_primary_reads
        49.9
        G174REL_M2_statistics_for_primary_unique_reads
        45.6
        G174REL_M3_G174REL_M3
        86.9%
        21.9
        G174REL_M3_sorted
        94.9%
        20.8
        G174REL_M3_statistics_for_all_accepted_reads
        55.2
        G174REL_M3_statistics_for_primary_reads
        47.5
        G174REL_M3_statistics_for_primary_unique_reads
        43.4
        G174REL_M4_G174REL_M4
        72.0%
        12.0
        G174REL_M4_sorted
        92.6%
        11.1
        G174REL_M4_statistics_for_all_accepted_reads
        34.1
        G174REL_M4_statistics_for_primary_reads
        27.0
        G174REL_M4_statistics_for_primary_unique_reads
        23.7
        G174REL_M5_G174REL_M5
        84.5%
        27.5
        G174REL_M5_sorted
        94.2%
        25.9
        G174REL_M5_statistics_for_all_accepted_reads
        71.1
        G174REL_M5_statistics_for_primary_reads
        60.1
        G174REL_M5_statistics_for_primary_unique_reads
        54.4
        G174REL_M6_G174REL_M6
        78.6%
        17.6
        G174REL_M6_sorted
        93.5%
        16.5
        G174REL_M6_statistics_for_all_accepted_reads
        47.8
        G174REL_M6_statistics_for_primary_reads
        39.2
        G174REL_M6_statistics_for_primary_unique_reads
        34.8
        G174REL_M7_G174REL_M7
        87.5%
        26.3
        G174REL_M7_sorted
        94.6%
        24.9
        G174REL_M7_statistics_for_all_accepted_reads
        65.8
        G174REL_M7_statistics_for_primary_reads
        57.0
        G174REL_M7_statistics_for_primary_unique_reads
        51.9
        G174REL_M8_G174REL_M8
        88.9%
        25.9
        G174REL_M8_sorted
        94.4%
        24.5
        G174REL_M8_statistics_for_all_accepted_reads
        64.5
        G174REL_M8_statistics_for_primary_reads
        56.0
        G174REL_M8_statistics_for_primary_unique_reads
        51.2
        G174REL_M9_G174REL_M9
        79.7%
        11.5
        G174REL_M9_sorted
        93.1%
        10.7
        G174REL_M9_statistics_for_all_accepted_reads
        31.0
        G174REL_M9_statistics_for_primary_reads
        25.6
        G174REL_M9_statistics_for_primary_unique_reads
        22.7
        G175REL_M10_G175REL_M10
        90.4%
        14.3
        G175REL_M10_sorted
        95.3%
        13.6
        G175REL_M10_statistics_for_all_accepted_reads
        33.7
        G175REL_M10_statistics_for_primary_reads
        30.2
        G175REL_M10_statistics_for_primary_unique_reads
        28.2
        G175REL_M11_G175REL_M11
        89.6%
        13.7
        G175REL_M11_sorted
        94.5%
        12.9
        G175REL_M11_statistics_for_all_accepted_reads
        32.6
        G175REL_M11_statistics_for_primary_reads
        29.1
        G175REL_M11_statistics_for_primary_unique_reads
        27.0
        G175REL_M12_G175REL_M12
        90.1%
        16.7
        G175REL_M12_sorted
        94.3%
        15.8
        G175REL_M12_statistics_for_all_accepted_reads
        40.1
        G175REL_M12_statistics_for_primary_reads
        35.6
        G175REL_M12_statistics_for_primary_unique_reads
        33.1
        G175REL_M13_G175REL_M13
        88.8%
        11.3
        G175REL_M13_sorted
        94.3%
        10.6
        G175REL_M13_statistics_for_all_accepted_reads
        27.0
        G175REL_M13_statistics_for_primary_reads
        24.0
        G175REL_M13_statistics_for_primary_unique_reads
        22.3
        G175REL_M1_G175REL_M1
        83.3%
        17.3
        G175REL_M1_sorted
        93.9%
        16.3
        G175REL_M1_statistics_for_all_accepted_reads
        43.8
        G175REL_M1_statistics_for_primary_reads
        37.5
        G175REL_M1_statistics_for_primary_unique_reads
        34.1
        G175REL_M2_G175REL_M2
        83.9%
        15.7
        G175REL_M2_sorted
        94.3%
        14.8
        G175REL_M2_statistics_for_all_accepted_reads
        39.3
        G175REL_M2_statistics_for_primary_reads
        33.9
        G175REL_M2_statistics_for_primary_unique_reads
        30.9
        G175REL_M3_G175REL_M3
        87.5%
        22.0
        G175REL_M3_sorted
        93.0%
        20.5
        G175REL_M3_statistics_for_all_accepted_reads
        54.0
        G175REL_M3_statistics_for_primary_reads
        47.3
        G175REL_M3_statistics_for_primary_unique_reads
        43.4
        G175REL_M4_G175REL_M4
        82.1%
        17.4
        G175REL_M4_sorted
        94.7%
        16.5
        G175REL_M4_statistics_for_all_accepted_reads
        44.7
        G175REL_M4_statistics_for_primary_reads
        37.9
        G175REL_M4_statistics_for_primary_unique_reads
        34.3
        G175REL_M5_G175REL_M5
        87.2%
        15.6
        G175REL_M5_sorted
        94.1%
        14.6
        G175REL_M5_statistics_for_all_accepted_reads
        38.4
        G175REL_M5_statistics_for_primary_reads
        33.4
        G175REL_M5_statistics_for_primary_unique_reads
        30.7
        G175REL_M6_G175REL_M6
        85.7%
        15.5
        G175REL_M6_sorted
        94.6%
        14.6
        G175REL_M6_statistics_for_all_accepted_reads
        38.0
        G175REL_M6_statistics_for_primary_reads
        33.2
        G175REL_M6_statistics_for_primary_unique_reads
        30.5
        G175REL_M7_G175REL_M7
        88.7%
        16.8
        G175REL_M7_sorted
        94.7%
        15.9
        G175REL_M7_statistics_for_all_accepted_reads
        40.7
        G175REL_M7_statistics_for_primary_reads
        35.9
        G175REL_M7_statistics_for_primary_unique_reads
        33.1
        G175REL_M8_G175REL_M8
        90.1%
        16.3
        G175REL_M8_sorted
        95.1%
        15.5
        G175REL_M8_statistics_for_all_accepted_reads
        38.4
        G175REL_M8_statistics_for_primary_reads
        34.5
        G175REL_M8_statistics_for_primary_unique_reads
        32.1
        G175REL_M9_G175REL_M9
        85.9%
        16.1
        G175REL_M9_sorted
        94.4%
        15.2
        G175REL_M9_statistics_for_all_accepted_reads
        40.2
        G175REL_M9_statistics_for_primary_reads
        34.7
        G175REL_M9_statistics_for_primary_unique_reads
        31.7
        G176REL_M10_G176REL_M10
        86.7%
        14.2
        G176REL_M10_sorted
        94.1%
        13.4
        G176REL_M10_statistics_for_all_accepted_reads
        34.7
        G176REL_M10_statistics_for_primary_reads
        30.7
        G176REL_M10_statistics_for_primary_unique_reads
        28.1
        G176REL_M11_G176REL_M11
        88.1%
        16.9
        G176REL_M11_sorted
        93.5%
        15.8
        G176REL_M11_statistics_for_all_accepted_reads
        41.0
        G176REL_M11_statistics_for_primary_reads
        36.5
        G176REL_M11_statistics_for_primary_unique_reads
        33.4
        G176REL_M12_G176REL_M12
        88.9%
        16.5
        G176REL_M12_sorted
        95.1%
        15.7
        G176REL_M12_statistics_for_all_accepted_reads
        39.4
        G176REL_M12_statistics_for_primary_reads
        35.2
        G176REL_M12_statistics_for_primary_unique_reads
        32.5
        G176REL_M13_G176REL_M13
        88.3%
        15.0
        G176REL_M13_sorted
        94.7%
        14.2
        G176REL_M13_statistics_for_all_accepted_reads
        35.6
        G176REL_M13_statistics_for_primary_reads
        31.9
        G176REL_M13_statistics_for_primary_unique_reads
        29.6
        G176REL_M1_G176REL_M1
        81.4%
        16.1
        G176REL_M1_sorted
        94.0%
        15.1
        G176REL_M1_statistics_for_all_accepted_reads
        40.9
        G176REL_M1_statistics_for_primary_reads
        34.9
        G176REL_M1_statistics_for_primary_unique_reads
        31.6
        G176REL_M2_G176REL_M2
        82.7%
        17.1
        G176REL_M2_sorted
        95.1%
        16.2
        G176REL_M2_statistics_for_all_accepted_reads
        42.3
        G176REL_M2_statistics_for_primary_reads
        36.8
        G176REL_M2_statistics_for_primary_unique_reads
        33.6
        G176REL_M3_G176REL_M3
        86.5%
        13.3
        G176REL_M3_sorted
        95.2%
        12.7
        G176REL_M3_statistics_for_all_accepted_reads
        32.4
        G176REL_M3_statistics_for_primary_reads
        28.5
        G176REL_M3_statistics_for_primary_unique_reads
        26.2
        G176REL_M4_G176REL_M4
        83.1%
        16.7
        G176REL_M4_sorted
        95.8%
        16.0
        G176REL_M4_statistics_for_all_accepted_reads
        41.4
        G176REL_M4_statistics_for_primary_reads
        36.0
        G176REL_M4_statistics_for_primary_unique_reads
        33.0
        G176REL_M5_G176REL_M5
        86.0%
        23.2
        G176REL_M5_sorted
        95.7%
        22.2
        G176REL_M5_statistics_for_all_accepted_reads
        56.8
        G176REL_M5_statistics_for_primary_reads
        49.9
        G176REL_M5_statistics_for_primary_unique_reads
        45.9
        G176REL_M6_G176REL_M6
        85.0%
        12.9
        G176REL_M6_sorted
        95.3%
        12.3
        G176REL_M6_statistics_for_all_accepted_reads
        31.2
        G176REL_M6_statistics_for_primary_reads
        27.5
        G176REL_M6_statistics_for_primary_unique_reads
        25.4
        G176REL_M7_G176REL_M7
        89.2%
        24.6
        G176REL_M7_sorted
        94.3%
        23.2
        G176REL_M7_statistics_for_all_accepted_reads
        58.2
        G176REL_M7_statistics_for_primary_reads
        52.3
        G176REL_M7_statistics_for_primary_unique_reads
        48.4
        G176REL_M8_G176REL_M8
        90.1%
        18.6
        G176REL_M8_sorted
        95.2%
        17.7
        G176REL_M8_statistics_for_all_accepted_reads
        43.7
        G176REL_M8_statistics_for_primary_reads
        39.5
        G176REL_M8_statistics_for_primary_unique_reads
        36.8
        G176REL_M9_G176REL_M9
        85.9%
        10.6
        G176REL_M9_sorted
        95.2%
        10.1
        G176REL_M9_statistics_for_all_accepted_reads
        25.9
        G176REL_M9_statistics_for_primary_reads
        22.8
        G176REL_M9_statistics_for_primary_unique_reads
        21.0
        G177REL_M10_G177REL_M10
        79.4%
        41.8
        G177REL_M10_sorted
        67.4%
        28.1
        G177REL_M10_statistics_for_all_accepted_reads
        108.7
        G177REL_M10_statistics_for_primary_reads
        91.3
        G177REL_M10_statistics_for_primary_unique_reads
        80.9
        G177REL_M11_G177REL_M11
        84.2%
        42.7
        G177REL_M11_sorted
        64.2%
        27.4
        G177REL_M11_statistics_for_all_accepted_reads
        109.0
        G177REL_M11_statistics_for_primary_reads
        92.8
        G177REL_M11_statistics_for_primary_unique_reads
        82.6
        G177REL_M12_G177REL_M12
        83.3%
        31.7
        G177REL_M12_sorted
        65.7%
        20.8
        G177REL_M12_statistics_for_all_accepted_reads
        81.6
        G177REL_M12_statistics_for_primary_reads
        69.2
        G177REL_M12_statistics_for_primary_unique_reads
        61.3
        G177REL_M13_G177REL_M13
        80.2%
        27.2
        G177REL_M13_sorted
        66.5%
        18.1
        G177REL_M13_statistics_for_all_accepted_reads
        71.0
        G177REL_M13_statistics_for_primary_reads
        59.6
        G177REL_M13_statistics_for_primary_unique_reads
        52.7
        G177REL_M1_G177REL_M1
        84.2%
        42.8
        G177REL_M1_sorted
        65.8%
        28.2
        G177REL_M1_statistics_for_all_accepted_reads
        110.6
        G177REL_M1_statistics_for_primary_reads
        93.7
        G177REL_M1_statistics_for_primary_unique_reads
        82.9
        G177REL_M2_G177REL_M2
        83.7%
        42.4
        G177REL_M2_sorted
        64.8%
        27.5
        G177REL_M2_statistics_for_all_accepted_reads
        110.4
        G177REL_M2_statistics_for_primary_reads
        92.9
        G177REL_M2_statistics_for_primary_unique_reads
        81.9
        G177REL_M3_G177REL_M3
        82.3%
        30.8
        G177REL_M3_sorted
        67.1%
        20.6
        G177REL_M3_statistics_for_all_accepted_reads
        80.0
        G177REL_M3_statistics_for_primary_reads
        67.3
        G177REL_M3_statistics_for_primary_unique_reads
        59.4
        G177REL_M4_G177REL_M4
        83.7%
        33.1
        G177REL_M4_sorted
        63.5%
        21.0
        G177REL_M4_statistics_for_all_accepted_reads
        87.1
        G177REL_M4_statistics_for_primary_reads
        72.8
        G177REL_M4_statistics_for_primary_unique_reads
        64.1
        G177REL_M5_G177REL_M5
        82.4%
        36.5
        G177REL_M5_sorted
        63.6%
        23.2
        G177REL_M5_statistics_for_all_accepted_reads
        95.9
        G177REL_M5_statistics_for_primary_reads
        80.1
        G177REL_M5_statistics_for_primary_unique_reads
        70.5
        G177REL_M6_G177REL_M6
        83.6%
        35.0
        G177REL_M6_sorted
        66.0%
        23.1
        G177REL_M6_statistics_for_all_accepted_reads
        90.6
        G177REL_M6_statistics_for_primary_reads
        76.5
        G177REL_M6_statistics_for_primary_unique_reads
        67.7
        G177REL_M7_G177REL_M7
        81.8%
        35.6
        G177REL_M7_sorted
        62.8%
        22.3
        G177REL_M7_statistics_for_all_accepted_reads
        92.0
        G177REL_M7_statistics_for_primary_reads
        77.6
        G177REL_M7_statistics_for_primary_unique_reads
        68.7
        G177REL_M8_G177REL_M8
        82.5%
        31.0
        G177REL_M8_sorted
        68.7%
        21.3
        G177REL_M8_statistics_for_all_accepted_reads
        79.5
        G177REL_M8_statistics_for_primary_reads
        67.5
        G177REL_M8_statistics_for_primary_unique_reads
        60.1
        G177REL_M9_G177REL_M9
        86.4%
        18.1
        G177REL_M9_sorted
        66.9%
        12.1
        G177REL_M9_statistics_for_all_accepted_reads
        45.2
        G177REL_M9_statistics_for_primary_reads
        39.0
        G177REL_M9_statistics_for_primary_unique_reads
        35.0
        G178REL_M10_G178REL_M10
        84.8%
        24.3
        G178REL_M10_sorted
        83.3%
        20.2
        G178REL_M10_statistics_for_all_accepted_reads
        59.6
        G178REL_M10_statistics_for_primary_reads
        52.1
        G178REL_M10_statistics_for_primary_unique_reads
        47.0
        G178REL_M11_G178REL_M11
        85.4%
        19.1
        G178REL_M11_sorted
        88.5%
        16.9
        G178REL_M11_statistics_for_all_accepted_reads
        46.8
        G178REL_M11_statistics_for_primary_reads
        40.8
        G178REL_M11_statistics_for_primary_unique_reads
        36.8
        G178REL_M12_G178REL_M12
        85.8%
        20.6
        G178REL_M12_sorted
        87.0%
        17.9
        G178REL_M12_statistics_for_all_accepted_reads
        50.2
        G178REL_M12_statistics_for_primary_reads
        44.1
        G178REL_M12_statistics_for_primary_unique_reads
        39.8
        G178REL_M13_G178REL_M13
        84.8%
        18.6
        G178REL_M13_sorted
        81.6%
        15.2
        G178REL_M13_statistics_for_all_accepted_reads
        45.9
        G178REL_M13_statistics_for_primary_reads
        39.9
        G178REL_M13_statistics_for_primary_unique_reads
        36.0
        G178REL_M1_G178REL_M1
        85.4%
        21.9
        G178REL_M1_sorted
        81.3%
        17.8
        G178REL_M1_statistics_for_all_accepted_reads
        53.9
        G178REL_M1_statistics_for_primary_reads
        47.0
        G178REL_M1_statistics_for_primary_unique_reads
        42.4
        G178REL_M2_G178REL_M2
        86.0%
        17.6
        G178REL_M2_sorted
        85.5%
        15.1
        G178REL_M2_statistics_for_all_accepted_reads
        43.1
        G178REL_M2_statistics_for_primary_reads
        37.7
        G178REL_M2_statistics_for_primary_unique_reads
        34.2
        G178REL_M3_G178REL_M3
        86.7%
        18.5
        G178REL_M3_sorted
        86.7%
        16.0
        G178REL_M3_statistics_for_all_accepted_reads
        44.7
        G178REL_M3_statistics_for_primary_reads
        39.4
        G178REL_M3_statistics_for_primary_unique_reads
        35.8
        G178REL_M4_G178REL_M4
        85.3%
        20.6
        G178REL_M4_sorted
        81.2%
        16.7
        G178REL_M4_statistics_for_all_accepted_reads
        51.3
        G178REL_M4_statistics_for_primary_reads
        44.5
        G178REL_M4_statistics_for_primary_unique_reads
        40.1
        G178REL_M5_G178REL_M5
        84.6%
        27.7
        G178REL_M5_sorted
        83.9%
        23.3
        G178REL_M5_statistics_for_all_accepted_reads
        69.4
        G178REL_M5_statistics_for_primary_reads
        59.9
        G178REL_M5_statistics_for_primary_unique_reads
        53.7
        G178REL_M6_G178REL_M6
        84.1%
        24.3
        G178REL_M6_sorted
        88.1%
        21.4
        G178REL_M6_statistics_for_all_accepted_reads
        60.9
        G178REL_M6_statistics_for_primary_reads
        52.6
        G178REL_M6_statistics_for_primary_unique_reads
        47.1
        G178REL_M7_G178REL_M7
        85.4%
        20.2
        G178REL_M7_sorted
        83.4%
        16.8
        G178REL_M7_statistics_for_all_accepted_reads
        49.3
        G178REL_M7_statistics_for_primary_reads
        43.1
        G178REL_M7_statistics_for_primary_unique_reads
        38.9
        G178REL_M8_G178REL_M8
        85.0%
        21.4
        G178REL_M8_sorted
        87.8%
        18.8
        G178REL_M8_statistics_for_all_accepted_reads
        53.9
        G178REL_M8_statistics_for_primary_reads
        46.1
        G178REL_M8_statistics_for_primary_unique_reads
        41.3
        G178REL_M9_G178REL_M9
        84.7%
        19.9
        G178REL_M9_sorted
        88.4%
        17.6
        G178REL_M9_statistics_for_all_accepted_reads
        49.5
        G178REL_M9_statistics_for_primary_reads
        42.9
        G178REL_M9_statistics_for_primary_unique_reads
        38.5

        RSeQC

        RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

        Infer experiment

        Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

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        featureCounts

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

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        Samtools

        Samtools is a suite of programs for interacting with high-throughput sequencing data.

        Samtools Flagstat

        This module parses the output from samtools flagstat. All numbers in millions.

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        STAR

        STAR is an ultrafast universal RNA-seq aligner.

        Alignment Scores

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        MultiQC v1.11 - Written by Phil Ewels, available on GitHub.

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