Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    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

      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 hic_pro_psa_samples_multiqc_data_1 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:

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.12

        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 2024-01-12, 11:05 based on data in:

        General Statistics

        Showing 108/108 rows and 3/11 columns.
        Sample NameM Valid Pairs UniqueReported Read PairsTotal
        NRHV014XCD4_ARIMA
        231.1
        280.5
        404.5
        NRHV014XCD8_ARIMA
        162.2
        198.2
        280.8
        NRHV056CD8SF_ARIMA
        308.2
        393.5
        542.6
        NRHV073_CD4_ARIMA
        198.2
        256.1
        372.0
        NRHV073_CD8_ARIMA
        345.8
        439.3
        620.0
        NRHV079CD4_ARIMA
        250.4
        313.5
        440.8
        NRHV079CD8_ARIMA
        269.3
        340.2
        477.9
        NRHV086CD4_ARIMA
        237.4
        292.7
        420.9
        NRHV086CD8_ARIMA
        232.8
        285.9
        411.1
        NRHV121_CD4_ARIMA
        237.0
        302.1
        420.1
        NRHV121_CD8_ARIMA
        258.3
        336.5
        469.8
        NRHV151CD4_ARIMA
        120.5
        152.7
        229.6
        NRHV168CD4_ARIMA
        387.8
        485.0
        678.7
        NRHV168CD8_ARIMA
        168.6
        203.1
        290.4
        NRHV171CD4_ARIMA
        318.0
        416.8
        598.7
        NRHV171CD8_ARIMA
        186.7
        229.2
        326.3
        NRHV238_CD4_ARIMA
        179.0
        242.8
        347.2
        NRHV238_CD8_ARIMA
        242.0
        305.4
        428.3
        NRHV290CD4_ARIMA
        263.7
        324.4
        460.3
        NRHV290CD8_ARIMA
        228.0
        275.0
        392.6
        NRHV295CD4_ARIMA
        301.5
        381.1
        532.0
        NRHV295CD8_ARIMA
        189.4
        245.9
        336.5
        NRHV321_CD4_ARIMA
        290.2
        367.3
        515.6
        NRHV321_CD8_ARIMA
        279.7
        385.5
        537.1
        NRHV322_CD4_ARIMA
        192.5
        240.6
        342.0
        NRHV322_CD8_ARIMA
        180.7
        240.3
        338.2
        NRHV324CD4_ARIMA
        194.6
        243.0
        359.4
        NRHV324CD8_ARIMA
        200.9
        245.5
        363.2
        NRHV325CD4_ARIMA
        249.6
        308.9
        429.4
        NRHV325CD8_ARIMA
        273.2
        348.6
        499.3
        NRHV326CD4_ARIMA
        179.9
        221.2
        314.3
        NRHV326CD8_ARIMA
        174.9
        216.2
        308.4
        NRHV332CD4_ARIMA
        177.7
        233.7
        328.6
        NRHV332CD8_ARIMA
        198.9
        258.3
        373.9
        NRSF055CD8SF_ARIMA
        405.5
        524.5
        752.4
        PSA4920_CD4_ARIMA
        231.2
        297.9
        439.3
        PSA4920_CD8_ARIMA
        200.3
        307.4
        475.5
        PSA4941_CD8_ARIMA
        205.5
        257.4
        385.7
        PSA4942_CD4_ARIMA
        300.3
        387.9
        567.5
        PSA4942_CD8_ARIMA
        230.6
        292.4
        426.8
        PSA4943_CD8_ARIMA
        231.5
        292.3
        426.8
        PSA4944_CD4_ARIMA
        337.9
        437.8
        631.4
        PSA4945CD4_ARIMA
        265.3
        337.5
        479.9
        PSA4951CD8SF_ARIMA
        128.1
        175.5
        244.4
        PSA4954_CD8_ARIMA
        172.9
        220.1
        318.9
        PSA4958CD4SF_ARIMA
        578.1
        732.8
        1128.4
        PSA4958CD8SF_ARIMA
        507.3
        646.0
        957.8
        PSA4959_CD8_ARIMA
        271.9
        344.2
        496.2
        PSA4960_CD8_ARIMA
        215.3
        295.1
        447.5
        PSA4961_CD8_ARIMA
        225.3
        330.2
        509.8
        PSA4962_CD4_ARIMA
        144.8
        240.2
        360.1
        PSA4962_CD8_ARIMA
        216.7
        309.1
        463.1
        PSA4963_CD4_ARIMA
        248.5
        357.7
        535.1
        PSA4963_CD8_ARIMA
        242.2
        356.5
        541.5
        PSA4967CD4_ARIMA
        246.2
        313.8
        441.7
        PSA5008_CD4_ARIMA
        231.7
        310.2
        427.9
        PSA5008_CD8_ARIMA
        227.0
        305.1
        420.4
        PSA5010_CD4_ARIMA
        296.9
        379.4
        522.3
        PSA5012_CD4_ARIMA
        271.0
        359.1
        497.7
        PSA5012_CD8_ARIMA
        228.1
        323.6
        446.6
        PSA5025CD8SF_ARIMA
        124.5
        172.6
        257.8
        PSA5039CD8_ARIMA
        211.2
        294.5
        430.7
        PSA5040CD4_ARIMA
        344.8
        467.8
        688.2
        PsA4946CD8_ARIMA
        417.7
        528.7
        818.7
        PsA4950_CD4_ARIMA
        315.0
        423.2
        595.7
        PsA4950_CD8_ARIMA
        235.3
        299.9
        422.8
        PsA4951_CD4_ARIMA
        245.4
        308.4
        430.3
        PsA4951_CD8_ARIMA
        273.2
        349.8
        492.7
        PsA4954_CD4_ARIMA
        181.8
        242.6
        342.5
        PsA4957CD4_ARIMA
        299.5
        356.6
        508.0
        PsA4958CD4_ARIMA
        343.5
        426.0
        634.5
        PsA4958CD8_ARIMA
        302.3
        381.6
        617.3
        PsA4959CD4_ARIMA
        153.8
        209.0
        318.6
        PsA4959CD8SF_ARIMA
        387.7
        479.6
        707.8
        PsA4968CD4_ARIMA
        158.8
        193.2
        272.9
        PsA4968CD8_ARIMA
        293.0
        367.6
        514.5
        PsA4969CD8SF_ARIMA
        288.9
        352.7
        531.5
        PsA5006CD4_ARIMA
        98.1
        121.2
        168.7
        PsA5006CD8_ARIMA
        344.6
        428.0
        599.1
        PsA5007CD4_ARIMA
        183.8
        219.0
        309.5
        PsA5009CD4_ARIMA
        221.7
        286.0
        412.9
        PsA5009CD8_ARIMA
        169.3
        212.4
        312.7
        PsA5010CD8_ARIMA
        112.9
        141.5
        201.6
        PsA5013CD4_ARIMA
        148.2
        193.7
        296.1
        PsA5013CD8_ARIMA
        171.4
        206.7
        300.2
        PsA5014CD4_ARIMA
        238.6
        290.1
        415.8
        PsA5014CD8_ARIMA
        342.9
        422.3
        593.3
        PsA5015CD8_ARIMA
        179.0
        217.9
        311.0
        PsA5017CD4_ARIMA
        261.8
        318.3
        449.3
        PsA5017CD8_ARIMA
        279.1
        341.5
        486.0
        PsA5018CD4_ARIMA
        285.7
        378.6
        581.7
        PsA5018CD8_ARIMA
        366.0
        495.0
        730.3
        PsA5019CD4_ARIMA
        284.5
        361.7
        510.2
        PsA5019CD8_ARIMA
        201.6
        241.2
        340.2
        PsA5020CD8_ARIMA
        314.9
        422.8
        615.9
        PsA5021CD4_ARIMA
        165.4
        207.2
        302.1
        PsA5021CD8_ARIMA
        253.8
        346.8
        480.7
        PsA5022CD8_ARIMA
        239.0
        295.6
        436.9
        PsA5023CD8_ARIMA
        215.7
        266.6
        379.5
        PsA5024CD8_ARIMA
        197.8
        271.2
        388.6
        PsA5026CD4_ARIMA
        184.4
        218.5
        311.3
        PsA5026CD8_ARIMA
        159.4
        199.8
        284.5
        PsA5036CD8_ARIMA
        260.9
        316.2
        444.0
        PsA5037CD4_ARIMA
        273.7
        356.0
        532.8
        PsA5037CD8_ARIMA
        265.2
        353.3
        520.6
        PsA5040CD8_ARIMA
        195.2
        241.2
        340.9
        PsA5040CD8_SF_ARIMA
        225.4
        269.8
        375.6
        psa4944CD8_ARIMA
        239.1
        324.4
        464.7

        HiC-Pro

        HiC-Pro is an efficient and flexible pipeline for Hi-C data processing. The MultiQC module is supported since HiC-Pro v2.11.0.DOI: 10.1186/s13059-015-0831-x.

        Read Mapping

        Alignment of reads in single-end mode.

        HiC-Pro uses a two steps mapping strategy. End-to-end mapping is first performed (Full reads Alignments). Unmapped reads are then trimmed at their ligation site, and the 5' end is re-aligned on the reference genome (Trimmed Reads Alignments)

           
        loading..

        Read Pairing

        Pairing of single-end mapping.

        HiC-Pro combines aligned reads as pairs. Singleton, low quality pairs or pairs involving multi-mapped reads are usually discarded. Note that the filtering at pairing level can change accrding to the parameters used.

        loading..

        Read Pair Filtering

        Filtering of read pairs.

        Aligned read pairs are filtered to select valid 3C products from two different restriction fragments. Read pairs coming from the same fragments, such as self-ligation or unligated (danging-end) fragments, are discarded. Ligation products involving neighboring restriction fragment (religation) are also discarded. Filtered pairs correspond to ligation products discarded based on the range of insert/fragment sizes defined in the analysis. Finally, as the ligation should be a random process, valid read pairs from all orientations (R=Reverse, F=forward) are expected to be observed in the same proportion.

        loading..

        Contact Statistics

        Contacts statistics after duplicates removal.

        Description of contact frequency after duplicates removal. Intra-chromosomal (cis) interaction are expected to be more frequent than inter-chromosomal contacts (trans)

        loading..

        MultiQC v1.12 - Written by Phil Ewels, available on GitHub.

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