Loading report..

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_report_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:

        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 2025-09-05, 11:08 EDT based on data in: /vf/users/morellr/Projects/19_027Weisz_patchseq/results

        General Statistics

        Showing 62/62 rows and 9/11 columns.
        Sample Name% rRNA% mRNA% AlignedM Aligned% DuplicationM Reads After FilteringGC content% PF% Adapter
        LOC01.star
        4.7%
        49.3%
        84.0%
        1.8
        LOC01_fastp
        7.5%
        4.3
        47.1%
        99.5%
        0.9%
        LOC02.star
        5.4%
        74.8%
        74.7%
        1.8
        LOC02_fastp
        19.3%
        4.7
        47.2%
        99.2%
        1.0%
        LOC03.star
        14.3%
        51.4%
        85.0%
        1.9
        LOC03_fastp
        11.1%
        4.4
        49.4%
        99.3%
        0.7%
        LOC04.star
        7.9%
        67.3%
        82.3%
        1.1
        LOC04_fastp
        11.8%
        2.8
        48.3%
        99.4%
        0.9%
        LOC05.star
        4.6%
        65.5%
        84.4%
        2.3
        LOC05_fastp
        9.7%
        5.4
        48.1%
        99.2%
        0.9%
        LOC06.star
        29.1%
        45.0%
        81.2%
        1.4
        LOC06_fastp
        19.7%
        3.5
        49.6%
        99.2%
        22.0%
        LOC07.star
        18.3%
        47.8%
        79.3%
        1.3
        LOC07_fastp
        14.2%
        3.4
        48.7%
        99.0%
        25.5%
        LOC08.star
        7.7%
        65.9%
        87.6%
        1.6
        LOC08_fastp
        9.1%
        3.6
        47.8%
        99.2%
        19.7%
        LOC09.star
        11.8%
        75.8%
        85.0%
        1.5
        LOC09_fastp
        22.2%
        3.5
        46.5%
        99.0%
        25.0%
        LOC10.star
        16.3%
        48.7%
        83.9%
        1.3
        LOC10_fastp
        13.2%
        3.2
        47.5%
        99.3%
        26.3%
        LOC11.star
        10.1%
        75.6%
        83.0%
        1.0
        LOC11_fastp
        10.6%
        2.5
        47.6%
        99.7%
        0.7%
        LOC12.star
        13.6%
        67.5%
        84.0%
        1.0
        LOC12_fastp
        12.7%
        2.4
        47.5%
        99.6%
        0.8%
        LOC13.star
        8.1%
        66.4%
        87.2%
        1.2
        LOC13_fastp
        6.5%
        2.8
        48.3%
        99.7%
        0.7%
        LOC14.star
        15.6%
        54.5%
        89.4%
        1.3
        LOC14_fastp
        9.9%
        2.8
        49.4%
        99.5%
        1.4%
        LOC15.star
        4.9%
        75.0%
        90.6%
        1.3
        LOC15_fastp
        4.9%
        2.9
        50.1%
        99.6%
        0.9%
        LOC16.star
        13.0%
        75.2%
        75.4%
        0.7
        LOC16_fastp
        18.2%
        1.8
        45.8%
        99.6%
        0.7%
        LOC17.star
        8.8%
        84.6%
        81.0%
        1.1
        LOC17_fastp
        19.6%
        2.8
        47.8%
        99.6%
        0.9%
        LOC18.star
        13.0%
        67.7%
        85.9%
        1.2
        LOC18_fastp
        9.2%
        2.8
        48.1%
        99.5%
        0.8%
        MOC01.star
        14.2%
        56.1%
        80.5%
        1.8
        MOC01_fastp
        14.4%
        4.4
        48.1%
        99.5%
        0.8%
        MOC02.star
        14.7%
        50.7%
        73.2%
        1.8
        MOC02_fastp
        7.8%
        4.8
        53.4%
        99.4%
        0.7%
        MOC03.star
        12.6%
        76.3%
        85.7%
        1.7
        MOC03_fastp
        13.1%
        4.0
        50.3%
        99.4%
        0.7%
        MOC04.star
        26.5%
        38.3%
        74.5%
        1.5
        MOC04_fastp
        17.8%
        4.0
        51.5%
        99.2%
        0.8%
        MOC05.star
        4.7%
        44.4%
        92.8%
        1.4
        MOC05_fastp
        3.2%
        3.0
        46.2%
        99.2%
        1.0%
        MOC06.star
        10.8%
        74.2%
        83.2%
        1.0
        MOC06_fastp
        12.1%
        2.4
        49.5%
        99.3%
        0.9%
        MOC07.star
        20.3%
        67.1%
        82.3%
        3.8
        MOC07_fastp
        26.3%
        9.2
        49.0%
        99.2%
        20.4%
        MOC08.star
        8.7%
        82.7%
        85.6%
        1.8
        MOC08_fastp
        9.0%
        4.2
        50.4%
        99.2%
        20.2%
        MOC09.star
        18.0%
        65.7%
        83.1%
        1.5
        MOC09_fastp
        15.7%
        3.6
        49.1%
        99.1%
        23.1%
        MOC10.star
        21.6%
        61.1%
        83.1%
        1.5
        MOC10_fastp
        15.8%
        3.5
        50.2%
        99.1%
        20.2%
        MOC11.star
        18.2%
        65.1%
        79.2%
        1.5
        MOC11_fastp
        21.7%
        3.7
        48.0%
        99.2%
        24.1%
        MOC12.star
        14.9%
        56.6%
        83.3%
        1.5
        MOC12_fastp
        13.0%
        3.5
        48.5%
        99.3%
        22.5%
        MOC13.star
        8.3%
        56.7%
        86.0%
        1.2
        MOC13_fastp
        5.7%
        2.8
        50.0%
        99.5%
        1.2%

        Picard

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

        RnaSeqMetrics Assignment

        Number of bases in primary alignments that align to regions in the reference genome.

        loading..

        Gene Coverage

        loading..

        STAR

        STAR is an ultrafast universal RNA-seq aligner.DOI: 10.1093/bioinformatics/bts635.

        Alignment Scores

        loading..

        Gene Counts

        Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

           
        loading..

        fastp

        fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).DOI: 10.1093/bioinformatics/bty560.

        Filtered Reads

        Filtering statistics of sampled reads.

        loading..

        Insert Sizes

        Insert size estimation of sampled reads.

        loading..

        Sequence Quality

        Average sequencing quality over each base of all reads.

        loading..

        GC Content

        Average GC content over each base of all reads.

        loading..

        N content

        Average N content over each base of all reads.

        loading..

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

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