ATACseq-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 ATACseq-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

        ATACseq-cleaning-report

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

        Report generated on 2020-12-01, 02:56 based on data in: /share/workshop/epigenetics_workshop/msettles/atacseq_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 6/6 rows and 6/6 columns.
        Sample Name% PE% R1 Q30% R2 Q30GC ContentN ContentNotes
        JLAC003A_htsStats
        100.00%
        81.20%
        79.87%
        43.21%
        0.0948%
        initial Stats
        JLAC003B_htsStats
        100.00%
        81.25%
        78.59%
        43.49%
        0.1002%
        initial Stats
        JLAC003C_htsStats
        100.00%
        82.26%
        78.21%
        43.69%
        0.1001%
        initial Stats
        JLAC004D_htsStats
        100.00%
        89.27%
        87.50%
        43.81%
        0.1366%
        initial Stats
        JLAC004E_htsStats
        100.00%
        89.53%
        88.03%
        44.05%
        0.1355%
        initial Stats
        JLAC004F_htsStats
        100.00%
        88.64%
        87.50%
        43.99%
        0.1374%
        initial Stats

        Read Lengths: Paired End

        Distribution of read lengths for each sample.

        Notice: Each sample has a uniform read length distribution.
        Showing 6/6 rows and 2/2 columns.
        Sample NameR1 Read LengthsR2 Read Lengths
        JLAC003A_htsStats
        50
        50
        JLAC003B_htsStats
        50
        50
        JLAC003C_htsStats
        50
        50
        JLAC004D_htsStats
        50
        50
        JLAC004E_htsStats
        50
        50
        JLAC004F_htsStats
        50
        50

        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.

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        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.

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        hts_SeqScreener

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

        Showing 6/6 rows and 3/3 columns.
        Sample NamePE hits% PE HitsNotes
        JLAC003A_htsStats
        11
        0.0000%
        PhiX check
        JLAC003B_htsStats
        15
        0.0000%
        PhiX check
        JLAC003C_htsStats
        17
        0.0000%
        PhiX check
        JLAC004D_htsStats
        16
        0.0000%
        PhiX check
        JLAC004E_htsStats
        14
        0.0000%
        PhiX check
        JLAC004F_htsStats
        20
        0.0000%
        PhiX check

        hts_SuperDeduper

        A reference free duplicate read removal tool.

        Showing 6/6 rows and 3/3 columns.
        Sample Name% Duplicates% IgnoredNotes
        JLAC003A_htsStats
        23.48%
        3.10%
        Remove PCR duplicates
        JLAC003B_htsStats
        23.32%
        3.41%
        Remove PCR duplicates
        JLAC003C_htsStats
        18.81%
        3.06%
        Remove PCR duplicates
        JLAC004D_htsStats
        25.64%
        1.69%
        Remove PCR duplicates
        JLAC004E_htsStats
        19.02%
        1.56%
        Remove PCR duplicates
        JLAC004F_htsStats
        16.59%
        1.79%
        Remove PCR duplicates

        SuperDeduper: Duplicate Saturation

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

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        hts_AdapterTrimmer

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

        Showing 6/6 rows and 4/4 columns.
        Sample Name% Bp Lost% AdaptersAvg. Bps TrimmedNotes
        JLAC003A_htsStats
        3.38%
        39.39%
        8.57
        Overlap and remove adapters
        JLAC003B_htsStats
        3.43%
        38.66%
        8.87
        Overlap and remove adapters
        JLAC003C_htsStats
        4.90%
        52.01%
        9.43
        Overlap and remove adapters
        JLAC004D_htsStats
        3.55%
        40.64%
        8.73
        Overlap and remove adapters
        JLAC004E_htsStats
        4.41%
        47.85%
        9.21
        Overlap and remove adapters
        JLAC004F_htsStats
        5.69%
        60.63%
        9.39
        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 6/6 rows and 6/6 columns.
        Sample Name% Bp Lost% R1 of Bp Lost% R2 of Bp LostAvg. Bps Trimmed% DiscardedNotes
        JLAC003A_htsStats
        0.08%
        11.30%
        88.70%
        0.08
        0.00%
        Remove all Ns
        JLAC003B_htsStats
        0.09%
        10.96%
        89.04%
        0.08
        0.00%
        Remove all Ns
        JLAC003C_htsStats
        0.08%
        11.35%
        88.65%
        0.08
        0.00%
        Remove all Ns
        JLAC004D_htsStats
        0.07%
        5.33%
        94.67%
        0.07
        0.00%
        Remove all Ns
        JLAC004E_htsStats
        0.08%
        5.38%
        94.62%
        0.07
        0.00%
        Remove all Ns
        JLAC004F_htsStats
        0.07%
        5.29%
        94.71%
        0.07
        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.

           
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        hts_QWindowTrim

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

        Showing 6/6 rows and 5/5 columns.
        Sample Name% Bp Lost% R1 of Bp Lost% R2 of Bp LostAvg. Bps TrimmedNotes
        JLAC003A_htsStats
        4.81%
        36.06%
        63.94%
        4.65
        Quality trim
        JLAC003B_htsStats
        5.35%
        33.01%
        66.99%
        5.17
        Quality trim
        JLAC003C_htsStats
        4.79%
        30.78%
        69.22%
        4.55
        Quality trim
        JLAC004D_htsStats
        3.07%
        31.95%
        68.05%
        2.96
        Quality trim
        JLAC004E_htsStats
        2.65%
        32.62%
        67.38%
        2.53
        Quality trim
        JLAC004F_htsStats
        2.46%
        34.54%
        65.46%
        2.32
        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 6/6 rows and 2/2 columns.
        Sample Name% PE LostNotes
        JLAC003A_htsStats
        36.80%
        Remove too short
        JLAC003B_htsStats
        37.51%
        Remove too short
        JLAC003C_htsStats
        42.16%
        Remove too short
        JLAC004D_htsStats
        31.60%
        Remove too short
        JLAC004E_htsStats
        33.96%
        Remove too short
        JLAC004F_htsStats
        39.39%
        Remove too short

        hts_Stats 2

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

        Showing 6/6 rows and 6/6 columns.
        Sample Name% PE% R1 Q30% R2 Q30GC ContentN ContentNotes
        JLAC003A_htsStats
        100.00%
        94.99%
        94.29%
        43.35%
        0.0000%
        end Stats
        JLAC003B_htsStats
        100.00%
        95.21%
        93.93%
        43.65%
        0.0000%
        end Stats
        JLAC003C_htsStats
        100.00%
        95.65%
        93.97%
        43.42%
        0.0000%
        end Stats
        JLAC004D_htsStats
        100.00%
        97.20%
        96.42%
        44.13%
        0.0000%
        end Stats
        JLAC004E_htsStats
        100.00%
        97.28%
        96.61%
        43.98%
        0.0000%
        end Stats
        JLAC004F_htsStats
        100.00%
        97.27%
        96.74%
        43.47%
        0.0000%
        end Stats

        Read Lengths: Paired End

        Distribution of read lengths for each sample.

        Notice: Each sample has a uniform read length distribution.
        Showing 6/6 rows and 2/2 columns.
        Sample NameR1 Read LengthsR2 Read Lengths
        JLAC003A_htsStats
        50
        50
        JLAC003B_htsStats
        50
        50
        JLAC003C_htsStats
        50
        50
        JLAC004D_htsStats
        50
        50
        JLAC004E_htsStats
        50
        50
        JLAC004F_htsStats
        50
        50

        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..