ChIPseq-cleaning-report

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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in ChIPseq-cleaning-report_multiqc_report_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 1.10.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

        ChIPseq-cleaning-report

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2020-12-01, 02:54 based on data in: /share/workshop/epigenetics_workshop/msettles/chipseq_example/01-HTS_Preproc


        HTStream

        HTStream quality control and processing pipeline for High Throughput Sequencing data.

        Processing Overview

        General statistics from the HTStream pipeline.


        Preprocessing Statistics

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        Fragment Reduction

        Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

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        Basepair Reduction

        Provides scaled statistics collected throughout the preprocessing pipeline, highlighting variable statistics across experiment.

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        hts_Stats

        Generates a JSON formatted file containing a set of statistical measures about the input read data.

        Showing 8/8 rows and 6/6 columns.
        Sample Name% PE% R1 Q30% R2 Q30GC ContentN ContentNotes
        JLDY037D_htsStats
        100.00%
        93.58%
        86.22%
        47.85%
        0.0104%
        initial Stats
        JLDY037E_htsStats
        100.00%
        95.10%
        84.75%
        46.01%
        0.0104%
        initial Stats
        JLDY037F_htsStats
        100.00%
        95.09%
        86.42%
        46.66%
        0.0105%
        initial Stats
        JLDY037G_htsStats
        100.00%
        94.41%
        86.40%
        46.88%
        0.0108%
        initial Stats
        JLDY037I_htsStats
        100.00%
        95.05%
        85.34%
        46.28%
        0.0107%
        initial Stats
        JLDY037J_htsStats
        100.00%
        93.86%
        86.33%
        44.32%
        0.0107%
        initial Stats
        JLDY037K_htsStats
        100.00%
        95.10%
        86.09%
        45.04%
        0.0107%
        initial Stats
        JLDY037L_htsStats
        100.00%
        61.56%
        58.96%
        45.31%
        0.0105%
        initial Stats

        Read Lengths: Paired End

        Distribution of read lengths for each sample.

        Notice: Each sample has a uniform read length distribution.
        Showing 8/8 rows and 2/2 columns.
        Sample NameR1 Read LengthsR2 Read Lengths
        JLDY037D_htsStats
        151
        151
        JLDY037E_htsStats
        151
        151
        JLDY037F_htsStats
        151
        151
        JLDY037G_htsStats
        151
        151
        JLDY037I_htsStats
        151
        151
        JLDY037J_htsStats
        151
        151
        JLDY037K_htsStats
        151
        151
        JLDY037L_htsStats
        151
        151

        Base by Cycle: Paired End

        Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

        loading..

        Quality by Cycle: Paired End

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

        loading..

        hts_SeqScreener

        A simple sequence screening tool which uses a kmer lookup approach to identify reads from an unwanted source.

        Showing 8/8 rows and 3/3 columns.
        Sample NamePE hits% PE HitsNotes
        JLDY037D_htsStats
        43810
        0.1095%
        PhiX check
        JLDY037E_htsStats
        21933
        0.0778%
        PhiX check
        JLDY037F_htsStats
        30137
        0.0742%
        PhiX check
        JLDY037G_htsStats
        51143
        0.1469%
        PhiX check
        JLDY037I_htsStats
        51460
        0.1286%
        PhiX check
        JLDY037J_htsStats
        36712
        0.1146%
        PhiX check
        JLDY037K_htsStats
        46331
        0.1226%
        PhiX check
        JLDY037L_htsStats
        5958
        0.3030%
        PhiX check

        hts_SuperDeduper

        A reference free duplicate read removal tool.

        Showing 8/8 rows and 3/3 columns.
        Sample Name% Duplicates% IgnoredNotes
        JLDY037D_htsStats
        94.23%
        0.04%
        Remove PCR duplicates
        JLDY037E_htsStats
        30.68%
        0.04%
        Remove PCR duplicates
        JLDY037F_htsStats
        38.47%
        0.04%
        Remove PCR duplicates
        JLDY037G_htsStats
        52.73%
        0.04%
        Remove PCR duplicates
        JLDY037I_htsStats
        38.71%
        0.04%
        Remove PCR duplicates
        JLDY037J_htsStats
        32.84%
        0.04%
        Remove PCR duplicates
        JLDY037K_htsStats
        41.23%
        0.04%
        Remove PCR duplicates
        JLDY037L_htsStats
        91.15%
        0.04%
        Remove PCR duplicates

        SuperDeduper: Duplicate Saturation

        Plots the number of duplicates against the number of unique reads per sample.

        loading..

        hts_AdapterTrimmer

        Trims adapters which are sequenced when the fragment insert length is shorter than the read length.

        Showing 8/8 rows and 4/4 columns.
        Sample Name% Bp Lost% AdaptersAvg. Bps TrimmedNotes
        JLDY037D_htsStats
        0.90%
        3.99%
        67.93
        Overlap and remove adapters
        JLDY037E_htsStats
        0.83%
        4.15%
        60.04
        Overlap and remove adapters
        JLDY037F_htsStats
        0.85%
        4.23%
        60.38
        Overlap and remove adapters
        JLDY037G_htsStats
        0.68%
        3.36%
        61.29
        Overlap and remove adapters
        JLDY037I_htsStats
        1.10%
        5.59%
        59.37
        Overlap and remove adapters
        JLDY037J_htsStats
        0.86%
        4.23%
        61.09
        Overlap and remove adapters
        JLDY037K_htsStats
        0.78%
        3.91%
        60.43
        Overlap and remove adapters
        JLDY037L_htsStats
        2.60%
        9.48%
        83.00
        Overlap and remove adapters

        AdapterTrimmer: Trimmed Basepairs Composition

        Composition of basepairs trimmed from the ends of paired end and single end reads.

        loading..

        hts_NTrimmer

        Trims reads to the longest subsequence that contains no N's.

        Showing 8/8 rows and 6/6 columns.
        Sample Name% Bp Lost% R1 of Bp Lost% R2 of Bp LostAvg. Bps Trimmed% DiscardedNotes
        JLDY037D_htsStats
        0.02%
        45.01%
        54.99%
        0.05
        0.00%
        Remove all Ns
        JLDY037E_htsStats
        0.01%
        45.73%
        54.27%
        0.04
        0.00%
        Remove all Ns
        JLDY037F_htsStats
        0.01%
        45.67%
        54.33%
        0.04
        0.00%
        Remove all Ns
        JLDY037G_htsStats
        0.01%
        45.00%
        55.00%
        0.04
        0.00%
        Remove all Ns
        JLDY037I_htsStats
        0.01%
        45.43%
        54.57%
        0.04
        0.00%
        Remove all Ns
        JLDY037J_htsStats
        0.01%
        45.60%
        54.40%
        0.04
        0.00%
        Remove all Ns
        JLDY037K_htsStats
        0.01%
        45.21%
        54.79%
        0.04
        0.00%
        Remove all Ns
        JLDY037L_htsStats
        0.02%
        46.27%
        53.73%
        0.05
        0.00%
        Remove all Ns

        NTrimmer: Trimmed Basepairs Composition

        Plots the number of N bases trimmed from ends of paired end and single end reads.

           
        loading..

        hts_QWindowTrim

        Uses a sliding window approach to remove the low quality ends of reads.

        Showing 8/8 rows and 5/5 columns.
        Sample Name% Bp Lost% R1 of Bp Lost% R2 of Bp LostAvg. Bps TrimmedNotes
        JLDY037D_htsStats
        3.62%
        17.99%
        82.01%
        10.83
        Quality trim
        JLDY037E_htsStats
        1.17%
        17.50%
        82.50%
        3.51
        Quality trim
        JLDY037F_htsStats
        0.96%
        21.15%
        78.85%
        2.89
        Quality trim
        JLDY037G_htsStats
        1.08%
        21.94%
        78.06%
        3.24
        Quality trim
        JLDY037I_htsStats
        0.96%
        21.35%
        78.65%
        2.85
        Quality trim
        JLDY037J_htsStats
        1.04%
        23.28%
        76.72%
        3.11
        Quality trim
        JLDY037K_htsStats
        1.05%
        20.29%
        79.71%
        3.13
        Quality trim
        JLDY037L_htsStats
        27.84%
        25.77%
        74.23%
        81.87
        Quality trim

        QWindowTrim: Trimmed Basepairs Composition

        Plots the number of low quality basepairs trimmed from ends of paired end and single end reads.

           
        loading..

        hts_LengthFilter

        Discards reads below a minimum length threshold.

        Showing 8/8 rows and 2/2 columns.
        Sample Name% PE LostNotes
        JLDY037D_htsStats
        2.57%
        Remove too short
        JLDY037E_htsStats
        0.64%
        Remove too short
        JLDY037F_htsStats
        0.49%
        Remove too short
        JLDY037G_htsStats
        0.57%
        Remove too short
        JLDY037I_htsStats
        0.51%
        Remove too short
        JLDY037J_htsStats
        0.56%
        Remove too short
        JLDY037K_htsStats
        0.54%
        Remove too short
        JLDY037L_htsStats
        34.67%
        Remove too short

        hts_Stats 2

        Generates a JSON formatted file containing a set of statistical measures about the input read data.

        Showing 8/8 rows and 6/6 columns.
        Sample Name% PE% R1 Q30% R2 Q30GC ContentN ContentNotes
        JLDY037D_htsStats
        100.00%
        90.60%
        75.03%
        47.89%
        0.0000%
        end Stats
        JLDY037E_htsStats
        100.00%
        95.88%
        87.69%
        46.70%
        0.0000%
        end Stats
        JLDY037F_htsStats
        100.00%
        95.94%
        89.40%
        47.44%
        0.0000%
        end Stats
        JLDY037G_htsStats
        100.00%
        95.79%
        89.17%
        47.49%
        0.0000%
        end Stats
        JLDY037I_htsStats
        100.00%
        95.91%
        89.11%
        47.62%
        0.0000%
        end Stats
        JLDY037J_htsStats
        100.00%
        94.78%
        88.77%
        45.15%
        0.0000%
        end Stats
        JLDY037K_htsStats
        100.00%
        95.87%
        88.86%
        45.76%
        0.0000%
        end Stats
        JLDY037L_htsStats
        100.00%
        84.02%
        61.23%
        49.76%
        0.0000%
        end Stats

        Read Lengths: Paired End

        Distribution of read lengths for each sample.

        loading..

        Base by Cycle: Paired End

        Provides a measure of the uniformity of a distribution. The higher the average is at a certain position, the more unequal the base pair composition. N's are excluded from this calculation.

        loading..

        Quality by Cycle: Paired End

        Mean quality score for each position along the read. Sample is colored red if less than 60% of bps have mean score of at least Q30, orange if between 60% and 80%, and green otherwise.

        loading..