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        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 1.0.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 2022-09-26, 17:09 based on data in: /ptmp/LAS/hkaur/concatenated/multiqc_stats


        General Statistics

        Showing 8/8 rows and 6/8 columns.
        Sample Name% AlignedM Aligned% Trimmed% Dups% GCM Seqs
        Dif_D6_1_S4
        20.0%
        23.1
        38.3%
        90.7%
        51%
        115.4
        Dif_D6_2_S3
        21.7%
        24.5
        47.5%
        92.6%
        51%
        113.0
        Dif_D6_3_S2
        21.2%
        28.0
        37.1%
        93.0%
        51%
        131.8
        Dif_D6_4_S1
        19.5%
        23.1
        54.0%
        91.5%
        49%
        118.7
        Undif_D2_1_S8
        14.9%
        8.9
        56.3%
        97.3%
        50%
        59.7
        Undif_D2_2_S7
        16.9%
        21.1
        61.0%
        96.8%
        51%
        125.2
        Undif_D2_3_S6
        15.0%
        10.0
        35.2%
        94.6%
        51%
        66.9
        Undif_D2_4_S5
        17.0%
        13.5
        54.3%
        93.9%
        50%
        79.5

        STAR

        STAR is an ultrafast universal RNA-seq aligner.

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        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.

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        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.

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        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.

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        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.

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        Per Base N Content

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

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        Sequence Length Distribution

        All samples have sequences of a single length (76bp).


        Sequence Duplication Levels

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

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        Overrepresented sequences

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

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        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.

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