Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

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

        Choose Plots

        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

        Save Settings

        You can save the toolbox settings for this report to the browser.

        Load Settings

        Choose a saved report profile from the dropdown box below:

        About MultiQC

        This report was generated using MultiQC, version 1.8

        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 2021-02-27, 09:48 based on data in: /gscratch/scrubbed/sr320/021321-hw-bs

        Welcome! Not sure where to start?   Watch a tutorial video   (6:06)

        General Statistics

        Showing 24/24 rows and 6/8 columns.
        Sample Name% mCpG% mCHG% mCHHM C's% Dups% Aligned
        zr3644_10_R1
        10.9%
        0.5%
        0.5%
        669.8
        12.0%
        61.6%
        zr3644_11_R1
        10.6%
        0.5%
        0.5%
        722.6
        11.8%
        61.6%
        zr3644_12_R1
        9.7%
        0.5%
        0.5%
        610.2
        11.3%
        62.2%
        zr3644_13_R1
        10.5%
        0.5%
        0.5%
        706.2
        12.1%
        61.9%
        zr3644_14_R1
        11.8%
        0.5%
        0.5%
        484.8
        10.7%
        62.4%
        zr3644_15_R1
        11.2%
        0.5%
        0.5%
        768.3
        12.0%
        62.1%
        zr3644_16_R1
        10.6%
        0.5%
        0.5%
        630.6
        12.4%
        62.5%
        zr3644_17_R1
        10.5%
        0.5%
        0.5%
        747.1
        12.6%
        62.1%
        zr3644_18_R1
        10.7%
        0.5%
        0.5%
        677.8
        11.2%
        62.7%
        zr3644_19_R1
        10.3%
        0.5%
        0.5%
        649.2
        10.7%
        62.3%
        zr3644_1_R1
        9.7%
        0.5%
        0.5%
        652.5
        12.5%
        62.7%
        zr3644_20_R1
        10.4%
        0.5%
        0.5%
        703.0
        12.1%
        61.3%
        zr3644_21_R1
        10.5%
        0.5%
        0.5%
        668.8
        11.7%
        61.7%
        zr3644_22_R1
        10.4%
        0.5%
        0.5%
        626.0
        11.7%
        62.5%
        zr3644_23_R1
        10.3%
        0.5%
        0.5%
        521.1
        11.6%
        62.4%
        zr3644_24_R1
        10.4%
        0.5%
        0.5%
        693.8
        12.0%
        62.6%
        zr3644_2_R1
        10.3%
        0.5%
        0.5%
        732.2
        12.7%
        61.6%
        zr3644_3_R1
        10.4%
        0.5%
        0.5%
        517.6
        10.4%
        61.6%
        zr3644_4_R1
        10.1%
        0.5%
        0.5%
        644.8
        11.8%
        61.8%
        zr3644_5_R1
        10.5%
        0.5%
        0.5%
        587.3
        10.9%
        61.8%
        zr3644_6_R1
        10.4%
        0.5%
        0.5%
        698.0
        12.2%
        62.3%
        zr3644_7_R1
        10.6%
        0.5%
        0.5%
        1073.4
        11.5%
        61.6%
        zr3644_8_R1
        10.7%
        0.5%
        0.5%
        556.0
        10.9%
        61.9%
        zr3644_9_R1
        10.9%
        0.5%
        0.5%
        581.1
        12.6%
        61.9%

        Bismark

        Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

        Alignment Rates

        Created with Highcharts 5.0.6# ReadsChart context menuExport PlotBismark: Alignment ScoresAligned UniquelyAligned AmbiguouslyDid Not AlignNo Genomic Sequencezr3644_10_R1zr3644_11_R1zr3644_12_R1zr3644_13_R1zr3644_14_R1zr3644_15_R1zr3644_16_R1zr3644_17_R1zr3644_18_R1zr3644_19_R1zr3644_1_R1zr3644_20_R1zr3644_21_R1zr3644_22_R1zr3644_23_R1zr3644_24_R1zr3644_2_R1zr3644_3_R1zr3644_4_R1zr3644_5_R1zr3644_6_R1zr3644_7_R1zr3644_8_R1zr3644_9_R105M10M15M20M25M30M35M40M45M50M55M60M65M70M75M80M85M9…90MCreated with MultiQC

        Deduplication

        Created with Highcharts 5.0.6% ReadsChart context menuExport PlotBismark: DeduplicationDeduplicated reads (remaining)Duplicate reads (removed)zr3644_10_R1zr3644_11_R1zr3644_12_R1zr3644_13_R1zr3644_14_R1zr3644_15_R1zr3644_16_R1zr3644_17_R1zr3644_18_R1zr3644_19_R1zr3644_1_R1zr3644_20_R1zr3644_21_R1zr3644_22_R1zr3644_23_R1zr3644_24_R1zr3644_2_R1zr3644_3_R1zr3644_4_R1zr3644_5_R1zr3644_6_R1zr3644_7_R1zr3644_8_R1zr3644_9_R10102030405060708090100Created with MultiQC

        Strand Alignment

        Created with Highcharts 5.0.6% ReadsChart context menuExport PlotBismark: Alignment to Individual Bisulfite StrandsOriginal bottom strandComplementary to original bottom strandComplementary to original top strandOriginal top strandzr3644_10_R1zr3644_11_R1zr3644_12_R1zr3644_13_R1zr3644_14_R1zr3644_15_R1zr3644_16_R1zr3644_17_R1zr3644_18_R1zr3644_19_R1zr3644_1_R1zr3644_20_R1zr3644_21_R1zr3644_22_R1zr3644_23_R1zr3644_24_R1zr3644_2_R1zr3644_3_R1zr3644_4_R1zr3644_5_R1zr3644_6_R1zr3644_7_R1zr3644_8_R1zr3644_9_R10102030405060708090100Created with MultiQC

        Cytosine Methylation

        Hover over a data point for more information
        Created with Highcharts 5.0.60255075100Methylated CpG
        Created with Highcharts 5.0.60255075100Methylated CHG
        Created with Highcharts 5.0.60255075100Methylated CHH

        M-Bias

        This plot shows the average percentage methylation and coverage across reads. See the bismark user guide for more information on how these numbers are generated.

        Created with Highcharts 5.0.6Position (bp)% MethylationChart context menuExport PlotBismark: M-Bias0102030405060708090100110020406080100Created with MultiQC

        MultiQC v1.8 - Written by Phil Ewels, available on GitHub.

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