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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 1.0.dev0

        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 2024-11-28, 05:11 based on data in:

        General Statistics

        Showing 48/48 rows and 9/10 columns.
        Sample Name% AssignedM Assigned% AlignedM Aligned% Trimmed% Dups% GCLengthM Seqs
        A549_SC1
        74.3%
        0.8
        38.5%
        0.1
        78.3%
        87.7%
        49%
        46
        0.4
        A549_SC2
        75.2%
        0.7
        39.1%
        0.1
        76.4%
        88.0%
        49%
        48
        0.4
        A549_SC3
        66.8%
        0.8
        38.1%
        0.1
        73.4%
        87.6%
        49%
        48
        0.3
        A549_SC4
        68.5%
        0.3
        29.5%
        0.1
        80.2%
        85.1%
        52%
        38
        0.3
        A549_SC5
        70.3%
        1.0
        42.7%
        0.2
        70.6%
        90.1%
        48%
        50
        0.4
        A549_SC6
        71.1%
        0.8
        40.7%
        0.2
        75.3%
        87.5%
        49%
        48
        0.4
        BJ_SC1
        76.6%
        0.9
        38.9%
        0.1
        70.8%
        81.9%
        50%
        51
        0.3
        BJ_SC2
        74.8%
        0.5
        42.0%
        0.1
        77.6%
        81.3%
        49%
        47
        0.2
        BJ_SC3
        75.0%
        0.3
        26.4%
        0.1
        78.3%
        65.7%
        50%
        38
        0.2
        BJ_SC4
        76.7%
        0.6
        39.8%
        0.1
        75.1%
        83.0%
        49%
        48
        0.3
        BJ_SC5
        75.1%
        0.7
        41.5%
        0.1
        72.7%
        85.0%
        49%
        48
        0.3
        BJ_SC6
        65.0%
        0.3
        20.7%
        0.0
        79.3%
        79.1%
        52%
        40
        0.2
        HT29_SC1
        73.1%
        1.0
        46.1%
        0.2
        69.2%
        89.7%
        48%
        50
        0.5
        HT29_SC2
        70.8%
        0.8
        37.7%
        0.2
        73.9%
        83.7%
        49%
        45
        0.4
        HT29_SC3
        70.9%
        0.8
        41.9%
        0.2
        73.4%
        83.9%
        48%
        48
        0.4
        HT29_SC4
        71.9%
        1.0
        43.7%
        0.2
        70.6%
        86.9%
        49%
        49
        0.5
        HT29_SC5
        71.7%
        0.8
        44.1%
        0.2
        68.6%
        88.3%
        48%
        49
        0.4
        HT29_SC6
        77.6%
        1.0
        50.8%
        0.3
        60.0%
        87.9%
        47%
        49
        0.5
        HepG2_SC1
        82.4%
        1.3
        53.4%
        0.3
        60.4%
        90.0%
        47%
        55
        0.6
        HepG2_SC2
        75.7%
        0.8
        44.9%
        0.2
        69.6%
        88.3%
        47%
        50
        0.4
        HepG2_SC3
        75.5%
        1.0
        42.4%
        0.3
        61.3%
        85.7%
        48%
        50
        0.6
        HepG2_SC4
        77.2%
        0.7
        42.2%
        0.2
        70.4%
        87.6%
        48%
        50
        0.4
        HepG2_SC5
        74.4%
        0.8
        40.2%
        0.2
        71.6%
        88.1%
        48%
        50
        0.4
        HepG2_SC6
        74.7%
        0.9
        49.3%
        0.2
        67.1%
        86.5%
        48%
        53
        0.4
        Jurkat_SC1
        78.9%
        1.0
        57.2%
        0.3
        61.6%
        92.4%
        47%
        53
        0.5
        Jurkat_SC2
        80.7%
        0.7
        41.9%
        0.2
        76.7%
        89.3%
        49%
        48
        0.4
        Jurkat_SC3
        76.7%
        0.5
        32.4%
        0.1
        79.6%
        86.4%
        49%
        41
        0.3
        Jurkat_SC4
        82.1%
        0.4
        46.9%
        0.1
        73.8%
        84.6%
        48%
        48
        0.3
        Jurkat_SC5
        81.5%
        0.5
        48.0%
        0.1
        71.6%
        86.5%
        48%
        50
        0.3
        Jurkat_SC6
        79.4%
        0.5
        38.4%
        0.1
        76.4%
        87.2%
        49%
        44
        0.4
        KG1_SC1
        73.2%
        0.4
        40.5%
        0.1
        78.2%
        82.8%
        48%
        46
        0.3
        KG1_SC2
        68.8%
        0.6
        36.2%
        0.1
        72.7%
        82.4%
        50%
        47
        0.3
        KG1_SC3
        71.6%
        0.6
        39.2%
        0.2
        72.7%
        85.1%
        49%
        47
        0.4
        KG1_SC4
        68.3%
        0.8
        39.9%
        0.2
        68.2%
        87.3%
        49%
        48
        0.4
        KG1_SC5
        68.9%
        0.5
        39.6%
        0.1
        61.0%
        81.5%
        48%
        45
        0.4
        KG1_SC6
        68.4%
        0.6
        44.3%
        0.1
        62.8%
        82.8%
        49%
        52
        0.3
        REH_SC1
        77.7%
        0.4
        41.6%
        0.1
        79.4%
        83.3%
        48%
        45
        0.3
        REH_SC2
        76.2%
        0.3
        20.9%
        0.0
        85.4%
        78.7%
        52%
        37
        0.2
        REH_SC3
        77.6%
        0.4
        45.4%
        0.1
        74.6%
        80.1%
        46%
        47
        0.3
        REH_SC4
        77.4%
        0.5
        24.9%
        0.1
        75.1%
        63.2%
        51%
        37
        0.4
        REH_SC5
        60.9%
        0.7
        18.1%
        0.1
        62.3%
        68.9%
        53%
        39
        0.6
        REH_SC6
        77.8%
        0.3
        31.8%
        0.1
        81.4%
        76.7%
        50%
        42
        0.2
        THP-1_SC1
        79.4%
        0.6
        41.8%
        0.1
        71.2%
        80.4%
        49%
        49
        0.2
        THP-1_SC2
        82.1%
        0.5
        57.5%
        0.1
        70.1%
        81.8%
        47%
        52
        0.2
        THP-1_SC3
        80.3%
        0.2
        46.5%
        0.1
        74.8%
        71.6%
        48%
        48
        0.1
        THP-1_SC4
        79.4%
        0.4
        43.3%
        0.1
        78.2%
        76.4%
        49%
        48
        0.2
        THP-1_SC5
        63.7%
        0.2
        19.3%
        0.0
        88.2%
        75.6%
        52%
        35
        0.2
        THP-1_SC6
        73.2%
        0.3
        32.1%
        0.1
        83.2%
        77.8%
        50%
        42
        0.2

        featureCounts

        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.

        loading..

        STAR

        STAR is an ultrafast universal RNA-seq aligner.

        loading..

        Cutadapt

        Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

        This plot shows the number of reads with certain lengths of adapter trimmed. Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak may be related to adapter length. See the cutadapt documentation for more information on how these numbers are generated.

        loading..

        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

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

        loading..

        Per Sequence Quality Scores

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

        loading..

        Per Base Sequence Content

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

        Click a heatmap row to see a line plot for that dataset.

        rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

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

        loading..

        Per Base N Content

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

        loading..

        Sequence Length Distribution

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

        loading..

        Sequence Duplication Levels

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

        loading..

        Overrepresented sequences

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

        loading..

        Adapter Content

        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.

        No samples found with any adapter contamination > 0.1%

        MultiQC v1.0.dev0 - Written by Phil Ewels, available on GitHub.

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