Pryhuber_080318

Highlight Samples

This report has flat image plots that won't be highlighted.
See the documentation for help.

Regex mode off

    Rename Samples

    This report has flat image plots that won't be renamed.
    See the documentation for help.

    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

      This report has flat image plots that won't be hidden.
      See the documentation for help.

      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 Pryhuber_080318_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:

        About MultiQC

        This report was generated using MultiQC, version 1.5

        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

        Pryhuber_080318

        Project Type
        RNA-seq
        Library Preparation
        Clontech low input
        Sequencing Platform
        HiSeq 2500
        Data Formatting
        bcltofastq-2.19.0
        Data Cleaning
        Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
        Genome Alignment
        STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
        Reference Genome
        GRCh38 + gencode28
        Read Quantification1
        subread-1.6.1, featurecounts, -s 0 -t exon -g gene_name
        Read Quantification2
        subread-1.6.1, featurecounts, -M -s 0 -t exon -g gene_name

        Report generated on 2018-10-29, 09:43 based on data in: /gpfs/fs2/scratch/grc_group/current_projects/Project_Pryhuber_080318

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

        General Statistics

        Showing 151/151 rows and 10/11 columns.
        Sample NameM Raw Reads% Dropped% Dups% GCLengthM Seqs% AlignedM Aligned% AssignedM Assigned
        D008-CBL-END-XPA-1
        31.0
        2.7%
        60.1%
        46%
        94 bp
        30.2
        85.7%
        25.8
        61.4%
        23.4
        D008-CBL-EPI-XPA-1
        31.3
        3.0%
        58.7%
        46%
        94 bp
        30.3
        86.3%
        26.2
        62.5%
        22.1
        D008-CBL-MES-XPA-1
        32.8
        2.6%
        55.2%
        46%
        95 bp
        32.0
        91.2%
        29.1
        70.4%
        25.0
        D008-CBL-MIC-XPA-1
        34.3
        3.4%
        62.4%
        49%
        95 bp
        33.1
        91.8%
        30.4
        73.3%
        28.0
        D008-CBL-PMX-XPA-1
        26.6
        2.7%
        56.6%
        48%
        94 bp
        25.9
        89.5%
        23.2
        67.8%
        20.7
        D008-RML-BPS-XPA-1
        34.9
        2.7%
        56.7%
        47%
        95 bp
        33.9
        89.9%
        30.5
        65.4%
        26.6
        D011-CBL-END-XPA-1
        29.0
        2.6%
        59.4%
        45%
        94 bp
        28.2
        84.3%
        23.8
        60.0%
        21.5
        D011-CBL-EPI-XPA-1
        24.8
        3.8%
        67.4%
        38%
        91 bp
        23.9
        70.5%
        16.8
        47.7%
        13.9
        D011-CBL-MES-XPA-1
        26.3
        6.3%
        59.0%
        43%
        92 bp
        24.6
        80.6%
        19.9
        57.1%
        18.2
        D011-CBL-MIC-XPA-1
        30.8
        2.5%
        63.4%
        48%
        95 bp
        30.1
        88.8%
        26.7
        66.2%
        24.6
        D011-CBL-PMX-XPA-1
        32.0
        3.1%
        61.0%
        45%
        93 bp
        31.0
        83.7%
        25.9
        61.1%
        23.3
        D011-RML-BPS-XPA-1
        32.5
        2.6%
        54.0%
        48%
        95 bp
        31.7
        90.8%
        28.8
        64.7%
        24.2
        D018-BRR-PMX-XPA-1
        27.1
        2.9%
        51.7%
        48%
        95 bp
        26.3
        91.9%
        24.2
        75.7%
        23.0
        D018-CBL-END-XPA-2
        28.6
        3.4%
        63.4%
        42%
        94 bp
        27.7
        77.7%
        21.5
        58.0%
        19.2
        D018-CBL-EPI-XPA-1
        27.2
        4.9%
        81.5%
        34%
        94 bp
        25.9
        61.1%
        15.8
        50.0%
        15.5
        D018-CBL-MES-XPA-2
        31.7
        3.3%
        63.2%
        45%
        94 bp
        30.6
        82.5%
        25.3
        58.3%
        23.0
        D018-CBL-MIC-XPA-2
        26.8
        3.2%
        65.9%
        45%
        94 bp
        26.0
        82.4%
        21.4
        61.5%
        20.1
        D018-CBL-PMX-XPA-2
        31.0
        2.8%
        61.9%
        47%
        96 bp
        30.1
        89.1%
        26.8
        71.7%
        25.1
        D018-RML-BPS-XPA-3
        31.3
        3.1%
        55.8%
        47%
        94 bp
        30.4
        85.5%
        26.0
        49.6%
        20.7
        D019-BRR-PMX-XPA-1
        31.8
        3.3%
        61.0%
        44%
        94 bp
        30.7
        83.7%
        25.7
        65.5%
        23.5
        D019-CBL-END-XPA-1
        26.2
        3.0%
        58.5%
        44%
        95 bp
        25.5
        87.3%
        22.2
        72.5%
        20.7
        D019-CBL-EPI-XPA-1
        25.6
        2.8%
        60.3%
        44%
        94 bp
        24.9
        87.7%
        21.8
        70.1%
        19.9
        D019-CBL-MES-XPA-1
        30.4
        3.5%
        58.7%
        43%
        94 bp
        29.4
        80.9%
        23.8
        57.6%
        20.8
        D019-CBL-MIC-XPA-1
        31.6
        3.5%
        74.4%
        42%
        95 bp
        30.4
        78.4%
        23.9
        53.3%
        21.7
        D019-CBL-PMX-XPA-1
        25.9
        3.0%
        55.4%
        46%
        95 bp
        25.1
        89.3%
        22.4
        66.5%
        20.3
        D019-RML-BPS-XPA-1
        39.9
        3.2%
        53.7%
        47%
        96 bp
        38.6
        88.2%
        34.0
        57.6%
        28.7
        D022-BRR-PMX-XPA-1
        46.1
        3.1%
        68.9%
        48%
        95 bp
        44.6
        89.0%
        39.7
        70.0%
        38.3
        D022-CBL-END-XPA-1
        25.6
        3.1%
        55.1%
        47%
        95 bp
        24.8
        90.9%
        22.5
        68.2%
        19.8
        D022-CBL-EPI-XPA-1
        27.9
        3.7%
        65.9%
        43%
        95 bp
        26.8
        84.9%
        22.8
        71.8%
        21.4
        D022-CBL-MES-XPA-1
        27.7
        3.5%
        61.7%
        43%
        93 bp
        26.7
        80.7%
        21.6
        55.0%
        18.4
        D022-CBL-MIC-XPA-1
        27.8
        3.7%
        64.4%
        47%
        93 bp
        26.8
        86.8%
        23.2
        60.0%
        19.6
        D022-CBL-PMX-XPA-1
        29.9
        3.1%
        64.3%
        47%
        94 bp
        29.0
        85.9%
        24.9
        62.1%
        22.6
        D022-RML-BPS-XPA-3
        25.1
        3.1%
        52.2%
        45%
        92 bp
        24.3
        82.3%
        20.0
        42.7%
        15.0
        D024-BRR-PMX-XPA-1
        38.8
        4.1%
        63.3%
        47%
        95 bp
        37.3
        88.1%
        32.8
        68.5%
        31.1
        D024-CBL-END-XPA-2
        40.3
        4.2%
        63.4%
        47%
        95 bp
        38.6
        91.0%
        35.2
        70.6%
        32.3
        D024-CBL-EPI-XPA-2
        25.3
        4.1%
        58.4%
        44%
        93 bp
        24.3
        84.8%
        20.6
        63.1%
        18.3
        D024-CBL-MES-XPA-2
        40.8
        4.0%
        64.4%
        47%
        95 bp
        39.1
        88.4%
        34.6
        69.6%
        32.5
        D024-CBL-MIC-XPA-2
        35.0
        4.3%
        63.8%
        48%
        95 bp
        33.5
        90.9%
        30.5
        72.2%
        28.7
        D024-CBL-PMX-XPA-2
        34.9
        4.1%
        61.8%
        47%
        96 bp
        33.5
        91.0%
        30.5
        71.2%
        28.4
        D024-RML-BPS-XPA-1
        33.4
        5.2%
        49.2%
        47%
        94 bp
        31.7
        89.4%
        28.3
        54.8%
        21.1
        D031_CBL_END_XPA_2
        21.0
        3.2%
        50.7%
        47%
        95 bp
        20.4
        86.1%
        17.5
        59.5%
        15.9
        D031_CBL_EPI_XPA_2
        22.0
        3.6%
        77.5%
        41%
        93 bp
        21.2
        79.5%
        16.9
        64.3%
        17.5
        D031_CBL_MES_XPA_2
        19.7
        3.1%
        47.9%
        46%
        95 bp
        19.1
        86.3%
        16.5
        56.7%
        14.0
        D031_CBL_MIC_XPA_2
        25.6
        2.9%
        57.6%
        49%
        96 bp
        24.8
        87.5%
        21.7
        58.2%
        20.4
        D031_CBL_PMX_XPA_2
        20.1
        3.0%
        54.7%
        47%
        94 bp
        19.5
        83.9%
        16.4
        57.5%
        15.5
        D036-BRR-PMX-XPA-1
        26.2
        2.5%
        74.2%
        47%
        94 bp
        25.5
        83.6%
        21.3
        61.6%
        20.8
        D036-CBL-END-XPA-2
        24.7
        2.5%
        62.9%
        41%
        94 bp
        24.1
        76.5%
        18.4
        54.3%
        16.0
        D036-CBL-EPI-XPA-2
        25.6
        2.2%
        75.3%
        41%
        95 bp
        25.0
        79.5%
        19.9
        68.5%
        19.0
        D036-CBL-MES-XPA-2
        26.3
        2.2%
        63.8%
        43%
        94 bp
        25.7
        78.9%
        20.3
        55.5%
        17.8
        D036-CBL-MIC-XPA-2
        24.3
        3.2%
        61.0%
        49%
        95 bp
        23.5
        91.7%
        21.5
        71.8%
        19.8
        D036-CBL-PMX-XPA-2
        23.2
        2.2%
        60.5%
        47%
        94 bp
        22.7
        84.6%
        19.2
        61.2%
        17.0
        D038-BRR-PMX-XPA-1
        22.3
        3.2%
        67.1%
        44%
        93 bp
        21.6
        80.9%
        17.5
        59.0%
        16.4
        D038-CBL-END-XPA-1
        21.6
        2.6%
        56.0%
        43%
        95 bp
        21.0
        81.0%
        17.0
        57.4%
        14.1
        D038-CBL-EPI-XPA-1
        22.7
        2.5%
        59.0%
        44%
        94 bp
        22.1
        81.6%
        18.0
        54.0%
        15.5
        D038-CBL-MES-XPA-1
        21.3
        2.3%
        49.5%
        47%
        95 bp
        20.8
        88.7%
        18.4
        62.3%
        15.7
        D038-CBL-MIC-XPA-1
        22.2
        2.4%
        58.3%
        46%
        95 bp
        21.7
        84.9%
        18.4
        63.4%
        16.1
        D038-CBL-PMX-XPA-1
        22.5
        3.2%
        63.5%
        41%
        94 bp
        21.8
        73.4%
        16.0
        53.0%
        14.0
        D038-RML-BPS-XPA-1
        21.9
        2.4%
        48.2%
        45%
        93 bp
        21.4
        84.6%
        18.1
        54.9%
        14.8
        D041-BRR-PMX-XPA-1
        24.4
        2.5%
        64.0%
        45%
        94 bp
        23.8
        80.5%
        19.2
        56.8%
        18.5
        D041-CBL-END-XPA-1
        21.3
        2.6%
        51.8%
        47%
        96 bp
        20.8
        89.8%
        18.7
        64.4%
        15.8
        D041-CBL-EPI-XPA-1
        24.8
        3.8%
        66.0%
        36%
        90 bp
        23.9
        64.7%
        15.4
        37.7%
        12.1
        D041-CBL-MES-XPA-1
        25.5
        2.2%
        49.8%
        47%
        95 bp
        24.9
        90.6%
        22.6
        65.3%
        19.3
        D041-CBL-MIC-XPA-1
        23.2
        2.3%
        58.4%
        49%
        96 bp
        22.7
        90.5%
        20.5
        69.5%
        18.7
        D041-CBL-PMX-XPA-1
        29.3
        12.5%
        44.9%
        47%
        88 bp
        25.6
        90.9%
        23.3
        67.9%
        20.3
        D041-RML-BPS-XPA-1
        20.5
        2.3%
        55.3%
        49%
        96 bp
        20.0
        88.6%
        17.8
        62.3%
        15.6
        D043-BRR-PMX-XPA-1
        23.7
        2.8%
        71.0%
        47%
        94 bp
        23.0
        83.8%
        19.3
        61.5%
        18.4
        D043-CBL-END-XPA-1
        24.7
        2.8%
        57.7%
        44%
        94 bp
        24.1
        81.9%
        19.7
        55.8%
        16.4
        D043-CBL-EPI-XPA-1
        24.2
        5.1%
        72.8%
        43%
        93 bp
        22.9
        84.8%
        19.4
        72.6%
        19.7
        D043-CBL-MES-XPA-1
        24.8
        2.9%
        64.7%
        43%
        94 bp
        24.1
        80.2%
        19.3
        58.7%
        17.0
        D043-CBL-MIC-XPA-1
        23.9
        2.8%
        66.4%
        48%
        95 bp
        23.2
        88.6%
        20.6
        66.2%
        18.8
        D043-CBL-PMX-XPA-1
        25.0
        2.5%
        61.5%
        46%
        94 bp
        24.4
        85.5%
        20.8
        64.0%
        19.0
        D043-RML-BPS-XPA-1
        22.8
        2.6%
        51.6%
        45%
        93 bp
        22.2
        84.1%
        18.7
        57.0%
        15.9
        D044-BRR-PMX-XPA-1
        20.7
        2.6%
        62.3%
        47%
        94 bp
        20.2
        84.8%
        17.1
        62.4%
        16.5
        D044-CBL-END-XPA-1
        24.2
        5.5%
        52.9%
        47%
        92 bp
        22.9
        89.7%
        20.5
        67.8%
        18.0
        D044-CBL-EPI-XPA-1
        26.4
        2.5%
        54.6%
        46%
        94 bp
        25.7
        89.7%
        23.1
        67.6%
        20.4
        D044-CBL-MES-XPA-1
        24.2
        2.7%
        54.1%
        46%
        94 bp
        23.5
        89.8%
        21.1
        64.6%
        17.5
        D044-CBL-MIC-XPA-1
        34.0
        2.6%
        63.1%
        47%
        95 bp
        33.1
        88.3%
        29.2
        61.7%
        25.1
        D044-CBL-PMX-XPA-1
        32.0
        3.2%
        57.5%
        47%
        95 bp
        30.9
        90.2%
        27.9
        68.9%
        25.0
        D044-RML-BPS-XPA-1
        37.5
        3.0%
        55.2%
        46%
        95 bp
        36.3
        87.0%
        31.6
        53.0%
        25.3
        D056_CBL_END_XPA_2
        9.7
        26.9%
        29.8%
        45%
        84 bp
        7.1
        85.3%
        6.1
        52.4%
        5.0
        D056_CBL_EPI_XPA_2
        21.5
        2.9%
        72.3%
        45%
        94 bp
        20.9
        87.9%
        18.4
        71.9%
        18.7
        D056_CBL_MES_XPA_2
        19.5
        3.8%
        58.9%
        46%
        94 bp
        18.7
        84.7%
        15.9
        60.5%
        15.2
        D056_CBL_MIC_XPA_2
        23.8
        3.3%
        61.0%
        50%
        95 bp
        23.0
        87.2%
        20.0
        58.9%
        19.1
        D056_CBL_PMX_XPA_2
        22.4
        2.9%
        62.5%
        49%
        95 bp
        21.7
        86.8%
        18.9
        59.8%
        18.1
        D063_CBL_END_XPA_1
        23.8
        2.8%
        51.5%
        48%
        95 bp
        23.2
        87.6%
        20.3
        57.1%
        17.5
        D063_CBL_EPI_XPA_1
        20.8
        3.3%
        78.6%
        41%
        94 bp
        20.1
        75.9%
        15.3
        65.0%
        15.3
        D063_CBL_MES_XPA_1
        24.0
        2.9%
        55.5%
        46%
        95 bp
        23.3
        87.4%
        20.3
        66.3%
        18.1
        D063_CBL_MIC_XPA_1
        19.5
        2.8%
        57.7%
        50%
        95 bp
        18.9
        87.2%
        16.5
        58.5%
        15.7
        D063_CBL_PMX_XPA_1
        20.5
        2.9%
        58.1%
        48%
        95 bp
        19.9
        86.6%
        17.2
        59.5%
        16.3
        D071-BRR-PMX-XPA-1
        19.4
        2.1%
        52.9%
        47%
        95 bp
        19.0
        86.6%
        16.5
        61.7%
        14.7
        D071-RML-BPS-XPA-1
        19.6
        1.8%
        48.1%
        47%
        96 bp
        19.2
        88.8%
        17.1
        58.4%
        14.3
        D071-RML-END-XPA-1
        21.6
        2.0%
        52.9%
        48%
        95 bp
        21.1
        89.4%
        18.9
        64.9%
        16.7
        D071-RML-EPI-XPA-1
        22.5
        23.8%
        47.2%
        47%
        84 bp
        17.1
        86.6%
        14.8
        68.2%
        14.6
        D071-RML-MES-XPA-1
        22.1
        2.1%
        60.9%
        47%
        94 bp
        21.7
        85.8%
        18.6
        63.4%
        18.0
        D071-RML-MIC-XPA-1
        21.8
        3.1%
        73.8%
        47%
        94 bp
        21.1
        83.7%
        17.7
        61.0%
        16.5
        D071-RML-PMX-XPA-1
        18.7
        1.9%
        59.8%
        49%
        96 bp
        18.3
        89.5%
        16.4
        71.4%
        15.5
        D075_CBL_END_XPA_1
        23.7
        3.2%
        51.1%
        48%
        96 bp
        22.9
        91.1%
        20.9
        67.0%
        19.2
        D075_CBL_EPI_XPA_1
        22.3
        3.3%
        64.9%
        47%
        95 bp
        21.6
        88.1%
        19.0
        70.0%
        18.9
        D075_CBL_MES_XPA_1
        21.3
        4.8%
        45.4%
        48%
        94 bp
        20.3
        89.7%
        18.2
        61.7%
        15.9
        D075_CBL_MIC_XPA_1
        20.7
        3.3%
        55.8%
        50%
        95 bp
        20.0
        89.1%
        17.9
        62.7%
        16.7
        D075_CBL_PMX_XPA_1
        22.9
        3.4%
        50.8%
        48%
        95 bp
        22.1
        89.2%
        19.7
        63.4%
        17.9
        D092_CBL_END_XPA_1
        23.9
        3.0%
        53.6%
        48%
        96 bp
        23.2
        90.3%
        20.9
        65.0%
        19.0
        D092_CBL_EPI_XPA_1
        25.1
        3.5%
        72.7%
        45%
        94 bp
        24.3
        85.0%
        20.6
        70.5%
        21.4
        D092_CBL_MES_XPA_1
        19.8
        2.8%
        49.4%
        48%
        96 bp
        19.2
        90.0%
        17.3
        62.4%
        15.4
        D092_CBL_MIC_XPA_1
        21.3
        3.1%
        60.6%
        50%
        96 bp
        20.7
        88.7%
        18.3
        62.9%
        17.5
        D092_CBL_PMX_XPA_1
        21.5
        2.9%
        56.8%
        49%
        96 bp
        20.9
        88.8%
        18.5
        63.9%
        17.5
        D105_CBL_END_XPA_2
        20.7
        2.8%
        45.1%
        48%
        95 bp
        20.1
        90.0%
        18.1
        59.4%
        15.3
        D105_CBL_EPI_XPA_2
        15.6
        10.1%
        68.9%
        43%
        90 bp
        14.0
        85.2%
        11.9
        71.2%
        12.1
        D105_CBL_MES_XPA_2
        20.4
        3.5%
        44.9%
        48%
        95 bp
        19.7
        88.7%
        17.5
        59.8%
        15.3
        D105_CBL_MIC_XPA_2
        21.7
        3.1%
        56.2%
        50%
        95 bp
        21.0
        87.5%
        18.3
        58.5%
        17.3
        D105_CBL_PMX_XPA_2
        17.8
        3.0%
        50.9%
        49%
        95 bp
        17.3
        88.2%
        15.2
        61.2%
        14.4
        D110_CBL_END_XPA_1
        19.5
        2.8%
        53.0%
        49%
        96 bp
        19.0
        90.1%
        17.1
        64.2%
        16.2
        D110_CBL_EPI_XPA_1
        22.6
        3.7%
        63.0%
        50%
        95 bp
        21.8
        88.7%
        19.3
        66.4%
        19.1
        D110_CBL_MES_XPA_1
        21.1
        3.0%
        47.2%
        48%
        95 bp
        20.4
        88.2%
        18.0
        56.1%
        15.7
        D110_CBL_MIC_XPA_1
        27.0
        3.0%
        61.3%
        50%
        95 bp
        26.2
        88.0%
        23.1
        60.6%
        22.3
        D110_CBL_PMX_XPA_1
        23.5
        3.0%
        56.0%
        49%
        95 bp
        22.8
        88.7%
        20.2
        63.4%
        19.5
        D113_CBL_END_XPA_1
        19.3
        4.7%
        48.8%
        48%
        95 bp
        18.4
        90.6%
        16.7
        68.1%
        15.8
        D113_CBL_EPI_XPA_1
        23.0
        3.3%
        58.4%
        50%
        95 bp
        22.2
        89.7%
        20.0
        68.9%
        19.4
        D113_CBL_MES_XPA_1
        22.1
        3.5%
        44.4%
        48%
        95 bp
        21.3
        90.5%
        19.3
        61.4%
        16.4
        D113_CBL_MIC_XPA_1
        21.2
        3.3%
        56.9%
        50%
        96 bp
        20.5
        90.1%
        18.5
        67.0%
        17.8
        D113_CBL_PMX_XPA_1
        24.9
        3.6%
        51.9%
        50%
        95 bp
        24.0
        90.0%
        21.6
        66.9%
        20.4
        D116_RML_END_XPA_2
        20.1
        2.9%
        41.8%
        46%
        94 bp
        19.5
        87.4%
        17.1
        48.0%
        12.1
        D116_RML_EPI_XPA_2
        22.4
        3.2%
        69.0%
        44%
        94 bp
        21.7
        84.6%
        18.4
        65.0%
        17.8
        D116_RML_MES_XPA_2
        23.7
        3.1%
        56.5%
        47%
        95 bp
        23.0
        85.0%
        19.5
        57.5%
        18.0
        D116_RML_MIC_XPA_2
        20.1
        3.0%
        59.4%
        50%
        95 bp
        19.5
        87.0%
        16.9
        59.0%
        16.4
        D116_RML_PMX_XPA_2
        21.1
        3.2%
        60.0%
        50%
        95 bp
        20.4
        86.4%
        17.6
        58.3%
        17.0
        D119_CBL_END_XPA_1
        23.1
        3.2%
        55.5%
        48%
        95 bp
        22.4
        88.4%
        19.8
        61.8%
        18.5
        D119_CBL_EPI_XPA_1
        20.3
        3.2%
        61.8%
        47%
        95 bp
        19.7
        88.7%
        17.5
        67.6%
        16.8
        D119_CBL_MES_XPA_1
        22.0
        3.5%
        46.7%
        48%
        95 bp
        21.2
        89.0%
        18.9
        58.1%
        16.1
        D119_CBL_MIC_XPA_1
        18.7
        4.0%
        53.4%
        49%
        95 bp
        18.0
        86.7%
        15.6
        56.4%
        14.5
        D119_CBL_PMX_XPA_1
        19.9
        4.8%
        47.9%
        48%
        94 bp
        18.9
        88.3%
        16.7
        59.5%
        15.0
        D133_CBL_END_XPA_1
        23.4
        3.2%
        49.0%
        46%
        95 bp
        22.6
        87.8%
        19.9
        58.9%
        16.1
        D133_CBL_EPI_XPA_1
        24.4
        3.6%
        81.1%
        42%
        94 bp
        23.5
        82.5%
        19.4
        75.3%
        20.2
        D133_CBL_MES_XPA_1
        19.5
        3.7%
        48.5%
        46%
        95 bp
        18.7
        86.9%
        16.3
        60.3%
        14.1
        D133_CBL_MIC_XPA_1
        23.0
        3.2%
        54.2%
        49%
        95 bp
        22.2
        87.9%
        19.5
        56.2%
        16.8
        D133_CBL_PMX_XPA_1
        18.7
        3.3%
        55.1%
        48%
        95 bp
        18.1
        86.9%
        15.7
        59.8%
        14.3
        D134_CBL_END_XPA_1
        20.4
        3.3%
        49.9%
        43%
        94 bp
        19.7
        79.6%
        15.7
        44.2%
        11.2
        D134_CBL_EPI_XPA_1
        18.9
        3.2%
        79.2%
        41%
        94 bp
        18.3
        83.7%
        15.4
        73.2%
        15.4
        D134_CBL_MES_XPA_1
        15.0
        9.8%
        58.8%
        41%
        91 bp
        13.6
        78.0%
        10.6
        54.3%
        9.6
        D134_CBL_MIC_XPA_1
        19.0
        3.0%
        53.2%
        49%
        95 bp
        18.4
        88.4%
        16.3
        58.5%
        14.6
        D134_CBL_PMX_XPA_1
        18.9
        2.9%
        55.5%
        48%
        96 bp
        18.4
        87.9%
        16.2
        61.0%
        14.7
        D136_CBL_END_XPA_1
        17.6
        5.9%
        44.8%
        46%
        93 bp
        16.6
        88.4%
        14.7
        57.5%
        12.4
        D136_CBL_EPI_XPA_1
        16.1
        3.0%
        62.3%
        43%
        94 bp
        15.6
        82.8%
        12.9
        55.6%
        10.8
        D136_CBL_MES_XPA_1
        20.0
        2.8%
        47.0%
        47%
        95 bp
        19.4
        86.9%
        16.9
        53.5%
        14.0
        D136_CBL_MIC_XPA_1
        21.1
        2.6%
        49.6%
        48%
        95 bp
        20.6
        88.2%
        18.1
        54.4%
        15.2
        D136_CBL_PMX_XPA_1
        10.1
        29.8%
        31.0%
        46%
        84 bp
        7.1
        86.2%
        6.1
        57.6%
        5.7
        D143_CBL_END_XPA_1
        21.9
        3.7%
        53.2%
        49%
        95 bp
        21.1
        91.3%
        19.3
        68.9%
        18.4
        D143_CBL_EPI_XPA_1
        17.1
        4.0%
        54.7%
        48%
        94 bp
        16.4
        88.7%
        14.6
        67.6%
        14.2
        D143_CBL_MES_XPA_1
        21.7
        2.9%
        50.0%
        48%
        96 bp
        21.1
        90.4%
        19.1
        63.8%
        17.4
        D143_CBL_MIC_XPA_1
        15.6
        12.4%
        49.0%
        49%
        90 bp
        13.7
        87.9%
        12.0
        63.0%
        11.7
        D143_CBL_PMX_XPA_1
        21.2
        3.2%
        53.3%
        49%
        95 bp
        20.5
        90.2%
        18.5
        67.6%
        17.8

        Trimmomatic

        Trimmomatic is a flexible read trimming tool for Illumina NGS data.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Quality Histograms
        151
        0
        0

        The mean quality value across each base position in the read. See the FastQC help.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores
        151
        0
        0

        The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content
        0
        30
        121

        The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content
        18
        82
        51

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. See the FastQC help.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content
        151
        0
        0

        The percentage of base calls at each position for which an N was called. See the FastQC help.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution
        0
        151
        0

        The distribution of fragment sizes (read lengths) found. See the FastQC help.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels
        1
        26
        124

        The relative level of duplication found for every sequence. See the FastQC help.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences
        0
        140
        11

        The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content
        151
        0
        0

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        STAR

        STAR is an ultrafast universal RNA-seq aligner.

        Alignment Scores

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FeatureCounts (Unique Reads)

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        FeatureCounts (Multi Mapping Reads)

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).