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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 1.12

        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 2024-06-03, 09:12 based on data in: /home/shared/8TB_HDD_03/sr320/github/paper-pycno-sswd-2021-2022/analyses/13-hisat-deseq2

        General Statistics

        Showing 32/32 rows.
        Sample Name% Aligned
        PSC-19_hisat03
        81.5%
        PSC-23_hisat03
        79.2%
        PSC-24_hisat03
        74.6%
        PSC-34_hisat03
        10.3%
        PSC-35_hisat03
        16.1%
        PSC-36_hisat03
        24.3%
        PSC-37_hisat03
        10.2%
        PSC-38_hisat03
        11.5%
        PSC-39_hisat03
        15.0%
        PSC-40_hisat03
        13.9%
        PSC-42_hisat03
        80.3%
        PSC-43_hisat03
        81.9%
        PSC-48_hisat03
        78.3%
        PSC-49_hisat03
        77.7%
        PSC-52_hisat03
        79.5%
        PSC-54_hisat03
        80.3%
        PSC-56_hisat03
        74.9%
        PSC-57_hisat03
        83.4%
        PSC-58_hisat03
        80.2%
        PSC-59_hisat03
        78.1%
        PSC-61_hisat03
        78.8%
        PSC-63_hisat03
        80.5%
        PSC-64_hisat03
        80.7%
        PSC-67_hisat03
        77.4%
        PSC-69_hisat03
        78.0%
        PSC-71_hisat03
        77.8%
        PSC-73_hisat03
        79.4%
        PSC-75_hisat03
        46.6%
        PSC-76_hisat03
        79.1%
        PSC-78_hisat03
        63.4%
        PSC-81_hisat03
        77.7%
        PSC-83_hisat03
        81.6%

        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.
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        MultiQC v1.12 - Written by Phil Ewels, available on GitHub.

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