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        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.

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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 1.4

        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 2018-04-03, 08:51 based on data in: /mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/alignment-metrics

        General Statistics

        Showing 3/3 rows and 5/6 columns.
        Sample NameM Reads Mapped% AlignedInsert SizeMedian CoverageBases ≥ 30X
        NaomicfDNA2_S2_R1
        141.0
        82%
        158 bp
        2.0X
        0%
        NaomicfDNA4_S3_R1
        142.1
        57%
        163 bp
        2.0X
        0%
        NaomicfDNA5_S1_R1
        106.1
        40%
        158 bp
        1.0X
        0%

        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        Alignment Summary

        Plase note that Picard's read counts are divided by two for paired-end data.

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        Insert Size

        Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

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        WGS Coverage

        The number of bases in the genome territory for each fold coverage. Note that final 1% of data is hidden to prevent very long tails.

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        WGS Filtered Bases

        For more information about the filtered categories, see the Picard documentation.

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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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        MultiQC v1.4 - Written by Phil Ewels, available on GitHub.

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