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        If you use plots from MultiQC in a publication or presentation, please cite:

        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

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        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 2024-07-23, 12:59 based on data in:

        General Statistics

        Showing 65/65 rows and 5/6 columns.
        Sample NameM Reads Mapped% AssignedM Assigned% AlignedM Aligned
        G174_M10_G174_M10
        79.0%
        21.2
        G174_M10_sorted
        94.4%
        20.0
        G174_M10_statistics_for_all_accepted_reads
        49.4
        G174_M10_statistics_for_primary_reads
        45.0
        G174_M10_statistics_for_primary_unique_reads
        42.4
        G174_M11_G174_M11
        80.4%
        26.2
        G174_M11_sorted
        94.7%
        24.8
        G174_M11_statistics_for_all_accepted_reads
        60.7
        G174_M11_statistics_for_primary_reads
        55.5
        G174_M11_statistics_for_primary_unique_reads
        52.3
        G174_M12_G174_M12
        80.9%
        19.2
        G174_M12_sorted
        95.3%
        18.3
        G174_M12_statistics_for_all_accepted_reads
        44.5
        G174_M12_statistics_for_primary_reads
        40.6
        G174_M12_statistics_for_primary_unique_reads
        38.4
        G174_M13_G174_M13
        73.6%
        17.7
        G174_M13_sorted
        94.0%
        16.6
        G174_M13_statistics_for_all_accepted_reads
        42.2
        G174_M13_statistics_for_primary_reads
        37.8
        G174_M13_statistics_for_primary_unique_reads
        35.4
        G174_M1_G174_M1
        62.4%
        12.7
        G174_M1_sorted
        94.1%
        12.0
        G174_M1_statistics_for_all_accepted_reads
        31.6
        G174_M1_statistics_for_primary_reads
        27.4
        G174_M1_statistics_for_primary_unique_reads
        25.4
        G174_M2_G174_M2
        76.8%
        21.3
        G174_M2_sorted
        95.5%
        20.3
        G174_M2_statistics_for_all_accepted_reads
        51.1
        G174_M2_statistics_for_primary_reads
        45.4
        G174_M2_statistics_for_primary_unique_reads
        42.6
        G174_M3_G174_M3
        79.7%
        20.1
        G174_M3_sorted
        95.5%
        19.2
        G174_M3_statistics_for_all_accepted_reads
        47.6
        G174_M3_statistics_for_primary_reads
        42.7
        G174_M3_statistics_for_primary_unique_reads
        40.2
        G174_M4_G174_M4
        64.3%
        10.7
        G174_M4_sorted
        93.5%
        10.0
        G174_M4_statistics_for_all_accepted_reads
        27.3
        G174_M4_statistics_for_primary_reads
        23.3
        G174_M4_statistics_for_primary_unique_reads
        21.5
        G174_M5_G174_M5
        76.4%
        24.9
        G174_M5_sorted
        94.9%
        23.6
        G174_M5_statistics_for_all_accepted_reads
        59.9
        G174_M5_statistics_for_primary_reads
        53.2
        G174_M5_statistics_for_primary_unique_reads
        49.7
        G174_M6_G174_M6
        69.5%
        15.6
        G174_M6_sorted
        94.3%
        14.7
        G174_M6_statistics_for_all_accepted_reads
        38.4
        G174_M6_statistics_for_primary_reads
        33.6
        G174_M6_statistics_for_primary_unique_reads
        31.1
        G174_M7_G174_M7
        77.8%
        23.4
        G174_M7_sorted
        95.3%
        22.3
        G174_M7_statistics_for_all_accepted_reads
        54.1
        G174_M7_statistics_for_primary_reads
        49.5
        G174_M7_statistics_for_primary_unique_reads
        46.8
        G174_M8_G174_M8
        80.2%
        23.4
        G174_M8_sorted
        95.1%
        22.3
        G174_M8_statistics_for_all_accepted_reads
        53.5
        G174_M8_statistics_for_primary_reads
        49.3
        G174_M8_statistics_for_primary_unique_reads
        46.8
        G174_M9_G174_M9
        72.3%
        10.4
        G174_M9_sorted
        93.6%
        9.8
        G174_M9_statistics_for_all_accepted_reads
        26.1
        G174_M9_statistics_for_primary_reads
        22.8
        G174_M9_statistics_for_primary_unique_reads
        20.9

        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.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.