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        Note that additional data was saved in multiqc_data when this report was generated.

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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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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.14

        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 2024-11-19, 17:50 PST based on data in:

        General Statistics

        Showing 63/63 rows.
        Sample Name% Aligned
        101112C14_hisat
        71.4%
        101112C4_hisat
        36.1%
        101112C9_hisat
        63.5%
        101112H14_hisat
        65.8%
        101112H4_hisat
        29.5%
        101112H9_hisat
        60.3%
        101112L14_hisat
        72.7%
        101112L4_hisat
        33.3%
        101112L9_hisat
        69.2%
        101112M14_hisat
        70.7%
        101112M4_hisat
        40.9%
        101112M9_hisat
        72.4%
        123C14_hisat
        63.0%
        123C4_hisat
        67.0%
        123C9_hisat
        74.6%
        123H14_hisat
        83.2%
        123H4_hisat
        35.5%
        123H9_hisat
        53.7%
        123L14_hisat
        81.5%
        123L4_hisat
        32.7%
        123L9_hisat
        57.1%
        123M4_hisat
        62.0%
        123M9_hisat
        44.5%
        131415C14_hisat
        66.8%
        131415C4_hisat
        47.7%
        131415C9_hisat
        61.9%
        131415H14_hisat
        66.4%
        131415H4_hisat
        27.4%
        131415H9_hisat
        58.5%
        131415L14_hisat
        70.3%
        131415L4_hisat
        0.2%
        131415L9_hisat
        61.8%
        131415M14_hisat
        76.7%
        131415M4_hisat
        44.0%
        131415M9_hisat
        58.1%
        13M14_hisat
        64.1%
        456C4_hisat
        24.6%
        456H4_hisat
        37.5%
        456H9_hisat
        47.5%
        456L14_hisat
        66.3%
        456L4_hisat
        24.8%
        456L9_hisat
        67.2%
        456M14_hisat
        63.0%
        456M4_hisat
        38.0%
        456M9_hisat
        56.4%
        45C14_hisat
        29.3%
        45C9_hisat
        66.1%
        45H14_hisat
        45.5%
        67C9_hisat
        44.9%
        6C14_hisat
        51.4%
        789C4_hisat
        8.9%
        789H14_hisat
        71.9%
        789H4_hisat
        47.6%
        789H9_hisat
        70.2%
        789L14_hisat
        76.4%
        789L4_hisat
        28.1%
        789L9_hisat
        67.5%
        789M14_hisat
        71.2%
        789M4_hisat
        43.9%
        7C14_hisat
        63.8%
        89C14_hisat
        76.2%
        89C9_hisat
        68.2%
        89M9_hisat
        53.7%

        Bowtie 2 / HiSAT2

        Bowtie 2 and HISAT2 are fast and memory-efficient tools for aligning sequencing reads against a reference genome. Unfortunately both tools have identical log output by default, so it is impossible to distiguish which tool was used. .DOI: 10.1038/nmeth.1923; 10.1038/nmeth.3317; 10.1038/s41587-019-0201-4.

        Paired-end alignments

        This plot shows the number of reads aligning to the reference in different ways.

        Please note that single mate alignment counts are halved to tally with pair counts properly.

        There are 6 possible types of alignment:

        • PE mapped uniquely: Pair has only one occurence in the reference genome.
        • PE mapped discordantly uniquely: Pair has only one occurence but not in proper pair.
        • PE one mate mapped uniquely: One read of a pair has one occurence.
        • PE multimapped: Pair has multiple occurence.
        • PE one mate multimapped: One read of a pair has multiple occurence.
        • PE neither mate aligned: Pair has no occurence.
        loading..

        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

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