Loading report..

Highlight Samples

This report has flat image plots that won't be highlighted.
See the documentation for help.

Regex mode off

    Rename Samples

    This report has flat image plots that won't be renamed.
    See the documentation for help.

    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

      This report has flat image plots that won't be hidden.
      See the documentation for help.

      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 multiqc_GRCz11_data 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:

        About MultiQC

        This report was generated using MultiQC, version 1.11

        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

        These samples were run by seq2science v0.6.1, a tool for easy preprocessing of NGS data.

        Take a look at our docs for info about how to use this report to the fullest.

        Workflow
        rna-seq
        Date
        January 12, 2022
        Project
        pt5
        Contact E-mail
        tessa.dewijs2@ru.nl

        Report generated on 2022-01-13, 01:22 based on data in:

        Change sample names:

        Show/Hide samples:

        General Statistics

        Showing 230/230 rows and 11/21 columns.
        Sample Name% DuplicationGC content% PF% AdapterInsert Size% Dups% MappedM Total seqsGenome coverageM Genome readsM MT genome reads
        1-4-somites-5
        1.6%
        45.4%
        100.0%
        0.0%
        223 bp
        7.7%
        100.0%
        12.7
        1.1 X
        14.5
        0.6
        14-19-somites-1
        1.5%
        45.0%
        100.0%
        0.0%
        224 bp
        7.4%
        100.0%
        10.8
        0.9 X
        11.9
        0.7
        14-19-somites-2
        1.8%
        45.0%
        100.0%
        0.0%
        223 bp
        8.9%
        100.0%
        12.2
        1.0 X
        13.4
        0.7
        14-19-somites-3
        1.8%
        44.8%
        100.0%
        0.0%
        228 bp
        7.9%
        100.0%
        12.7
        1.0 X
        14.3
        0.7
        14-19-somites-4
        1.6%
        45.4%
        100.0%
        0.0%
        224 bp
        7.9%
        100.0%
        12.9
        1.0 X
        14.0
        0.7
        14-19-somites-5
        1.7%
        45.2%
        100.0%
        0.0%
        231 bp
        7.7%
        100.0%
        12.5
        1.0 X
        13.8
        0.7
        20-25-somites-1
        2.1%
        45.3%
        100.0%
        0.0%
        235 bp
        8.5%
        100.0%
        11.3
        1.0 X
        13.4
        0.5
        20-25-somites-2
        2.3%
        45.1%
        100.0%
        0.0%
        217 bp
        8.8%
        100.0%
        12.1
        1.1 X
        14.5
        0.6
        20-25-somites-3
        1.7%
        45.3%
        100.0%
        0.0%
        230 bp
        7.3%
        100.0%
        13.5
        1.1 X
        15.2
        0.6
        20-25-somites-4
        1.4%
        45.8%
        100.0%
        0.0%
        236 bp
        6.4%
        100.0%
        11.4
        0.9 X
        12.8
        0.5
        20-25-somites-5
        1.5%
        45.5%
        100.0%
        0.0%
        236 bp
        6.6%
        100.0%
        12.9
        1.0 X
        14.3
        0.6
        Day-4-1
        1.3%
        44.9%
        100.0%
        0.0%
        243 bp
        6.2%
        100.0%
        11.3
        0.9 X
        12.1
        0.5
        Day-4-2
        1.5%
        44.7%
        100.0%
        0.0%
        243 bp
        6.3%
        100.0%
        10.3
        0.8 X
        11.2
        0.5
        Day-4-3
        1.3%
        45.1%
        100.0%
        0.0%
        234 bp
        6.2%
        100.0%
        12.7
        1.0 X
        13.4
        0.6
        Day-4-4
        1.3%
        44.8%
        100.0%
        0.0%
        234 bp
        6.1%
        100.0%
        11.1
        0.9 X
        12.0
        0.5
        Day-4-5
        1.4%
        44.9%
        100.0%
        0.0%
        236 bp
        6.2%
        100.0%
        11.1
        0.9 X
        11.9
        0.6
        Day-5-1
        1.4%
        44.9%
        100.0%
        0.0%
        248 bp
        6.7%
        100.0%
        10.2
        0.8 X
        11.0
        0.5
        Day-5-2
        1.3%
        44.9%
        100.0%
        0.0%
        236 bp
        6.4%
        100.0%
        10.0
        0.8 X
        10.8
        0.5
        Day-5-3
        1.4%
        44.9%
        100.0%
        0.0%
        237 bp
        6.6%
        100.0%
        10.7
        0.8 X
        11.5
        0.5
        Day-5-4
        1.3%
        44.9%
        100.0%
        0.0%
        246 bp
        6.4%
        100.0%
        9.7
        0.8 X
        10.5
        0.5
        Day-5-5
        1.4%
        44.6%
        100.0%
        0.0%
        238 bp
        6.7%
        100.0%
        9.5
        0.8 X
        10.3
        0.5
        ERR1442566
        0.7%
        45.1%
        96.4%
        1.5%
        ERR1442567
        0.5%
        45.4%
        96.6%
        1.8%
        ERR1442568
        0.6%
        45.4%
        97.3%
        2.5%
        ERR1442569
        0.6%
        45.7%
        97.1%
        2.7%
        ERR1442570
        0.6%
        45.4%
        96.6%
        1.5%
        ERR1442571
        0.4%
        45.6%
        96.8%
        1.6%
        ERR1442572
        0.7%
        45.3%
        96.3%
        1.6%
        ERR1442573
        0.5%
        45.9%
        96.8%
        1.5%
        ERR1442574
        0.5%
        45.8%
        96.8%
        1.4%
        ERR1442575
        0.5%
        45.8%
        96.9%
        1.4%
        ERR1442576
        0.6%
        45.0%
        97.1%
        1.7%
        ERR1442577
        0.4%
        45.8%
        97.2%
        2.0%
        ERR1442578
        0.5%
        45.3%
        96.8%
        1.7%
        ERR1442579
        0.5%
        45.3%
        96.7%
        1.7%
        ERR1442580
        0.5%
        45.4%
        96.6%
        2.0%
        ERR1442581
        0.4%
        45.2%
        96.9%
        1.7%
        ERR1442582
        0.5%
        45.2%
        96.9%
        1.4%
        ERR1442583
        0.6%
        45.4%
        96.8%
        1.5%
        ERR1442584
        0.6%
        45.0%
        96.7%
        1.7%
        ERR1442585
        0.4%
        46.0%
        97.1%
        1.9%
        ERR1442586
        0.6%
        44.6%
        96.8%
        1.5%
        ERR1442587
        0.4%
        44.9%
        97.0%
        1.5%
        ERR1442588
        0.5%
        44.6%
        96.8%
        1.3%
        ERR1442589
        0.5%
        44.7%
        97.0%
        1.5%
        ERR1442590
        0.7%
        44.2%
        96.4%
        1.4%
        ERR1442591
        0.4%
        44.9%
        96.9%
        1.3%
        ERR1442592
        0.5%
        44.7%
        96.9%
        1.3%
        ERR1442593
        0.4%
        45.1%
        97.1%
        1.7%
        ERR1442594
        0.5%
        44.8%
        97.0%
        1.5%
        ERR1442595
        0.4%
        44.9%
        97.0%
        1.6%
        ERR1442596
        0.5%
        44.9%
        96.6%
        1.3%
        ERR1442597
        0.4%
        44.9%
        97.0%
        1.6%
        ERR1442598
        0.4%
        44.9%
        97.0%
        1.4%
        ERR1442599
        0.5%
        44.9%
        96.8%
        1.2%
        ERR1442600
        0.5%
        44.6%
        96.9%
        1.4%
        ERR1442611
        0.4%
        45.0%
        96.6%
        2.1%
        ERR1442612
        0.5%
        45.0%
        96.5%
        2.0%
        ERR1442613
        0.6%
        44.8%
        96.5%
        1.9%
        ERR1442614
        0.5%
        45.4%
        96.8%
        1.9%
        ERR1442615
        0.5%
        45.2%
        96.7%
        1.5%
        ERR1442616
        0.7%
        45.4%
        96.2%
        1.4%
        ERR1442617
        0.7%
        45.1%
        96.7%
        2.5%
        ERR1442618
        0.4%
        45.4%
        96.9%
        1.7%
        ERR1442619
        0.4%
        45.8%
        96.8%
        1.6%
        ERR1442620
        0.4%
        45.5%
        96.9%
        1.7%
        ERR1442640
        0.4%
        45.4%
        96.9%
        1.8%
        ERR1442656
        0.7%
        45.1%
        96.4%
        1.5%
        ERR1442657
        0.5%
        45.4%
        96.6%
        1.8%
        ERR1442658
        0.6%
        45.4%
        97.3%
        2.4%
        ERR1442659
        0.6%
        45.6%
        97.1%
        2.7%
        ERR1442660
        0.6%
        45.3%
        96.6%
        1.5%
        ERR1442661
        0.4%
        45.6%
        96.7%
        1.6%
        ERR1442662
        0.7%
        45.3%
        96.3%
        1.6%
        ERR1442663
        0.5%
        45.8%
        96.8%
        1.4%
        ERR1442664
        0.5%
        45.8%
        96.8%
        1.4%
        ERR1442665
        0.5%
        45.8%
        96.9%
        1.4%
        ERR1442666
        0.6%
        45.0%
        97.1%
        1.7%
        ERR1442667
        0.4%
        45.8%
        97.2%
        2.0%
        ERR1442668
        0.4%
        45.3%
        96.8%
        1.7%
        ERR1442669
        0.5%
        45.3%
        96.7%
        1.7%
        ERR1442670
        0.5%
        45.4%
        96.6%
        2.0%
        ERR1442671
        0.4%
        45.2%
        96.9%
        1.7%
        ERR1442672
        0.5%
        45.2%
        96.9%
        1.4%
        ERR1442673
        0.6%
        45.3%
        96.8%
        1.5%
        ERR1442674
        0.6%
        45.0%
        96.7%
        1.7%
        ERR1442675
        0.4%
        46.0%
        97.1%
        2.0%
        ERR1442676
        0.5%
        44.6%
        96.8%
        1.5%
        ERR1442677
        0.4%
        44.9%
        96.9%
        1.5%
        ERR1442678
        0.5%
        44.5%
        96.8%
        1.3%
        ERR1442679
        0.5%
        44.6%
        97.0%
        1.5%
        ERR1442680
        0.7%
        44.2%
        96.4%
        1.4%
        ERR1442681
        0.4%
        44.9%
        96.9%
        1.4%
        ERR1442682
        0.5%
        44.7%
        96.9%
        1.2%
        ERR1442683
        0.4%
        45.1%
        97.0%
        1.6%
        ERR1442684
        0.5%
        44.8%
        97.0%
        1.5%
        ERR1442685
        0.4%
        44.9%
        97.0%
        1.6%
        ERR1442686
        0.5%
        44.9%
        96.7%
        1.3%
        ERR1442687
        0.4%
        44.9%
        96.9%
        1.5%
        ERR1442688
        0.5%
        44.9%
        97.0%
        1.4%
        ERR1442689
        0.5%
        44.9%
        96.8%
        1.2%
        ERR1442690
        0.6%
        44.6%
        96.9%
        1.4%
        ERR1442701
        0.4%
        45.0%
        96.6%
        2.1%
        ERR1442702
        0.5%
        45.0%
        96.5%
        2.0%
        ERR1442703
        0.6%
        44.8%
        96.5%
        1.9%
        ERR1442704
        0.5%
        45.4%
        96.8%
        1.9%
        ERR1442705
        0.5%
        45.2%
        96.7%
        1.5%
        ERR1442706
        0.7%
        45.3%
        96.2%
        1.4%
        ERR1442707
        0.7%
        45.1%
        96.6%
        2.5%
        ERR1442708
        0.5%
        45.3%
        96.9%
        1.7%
        ERR1442709
        0.4%
        45.8%
        96.8%
        1.5%
        ERR1442710
        0.4%
        45.5%
        96.9%
        1.7%
        ERR1442730
        0.4%
        45.4%
        96.9%
        1.8%
        ERR1442746
        0.7%
        45.1%
        96.0%
        1.5%
        ERR1442747
        0.5%
        45.4%
        96.2%
        1.8%
        ERR1442748
        0.7%
        45.4%
        96.8%
        2.4%
        ERR1442749
        0.6%
        45.6%
        96.7%
        2.7%
        ERR1442750
        0.6%
        45.4%
        96.1%
        1.5%
        ERR1442751
        0.4%
        45.6%
        96.3%
        1.6%
        ERR1442752
        0.7%
        45.3%
        95.8%
        1.7%
        ERR1442753
        0.5%
        45.8%
        96.3%
        1.4%
        ERR1442754
        0.5%
        45.8%
        96.3%
        1.4%
        ERR1442755
        0.5%
        45.8%
        96.4%
        1.4%
        ERR1442756
        0.6%
        45.0%
        96.6%
        1.7%
        ERR1442757
        0.4%
        45.8%
        96.7%
        2.0%
        ERR1442758
        0.5%
        45.3%
        96.3%
        1.7%
        ERR1442759
        0.5%
        45.3%
        96.3%
        1.7%
        ERR1442760
        0.5%
        45.4%
        96.2%
        1.9%
        ERR1442761
        0.4%
        45.2%
        96.4%
        1.7%
        ERR1442762
        0.6%
        45.2%
        96.5%
        1.4%
        ERR1442763
        0.6%
        45.4%
        96.3%
        1.5%
        ERR1442764
        0.6%
        45.0%
        96.3%
        1.7%
        ERR1442765
        0.4%
        46.0%
        96.6%
        1.9%
        ERR1442766
        0.6%
        44.6%
        96.4%
        1.5%
        ERR1442767
        0.4%
        44.9%
        96.5%
        1.5%
        ERR1442768
        0.5%
        44.6%
        96.3%
        1.3%
        ERR1442769
        0.5%
        44.7%
        96.5%
        1.5%
        ERR1442770
        0.7%
        44.2%
        96.0%
        1.3%
        ERR1442771
        0.5%
        44.9%
        96.5%
        1.3%
        ERR1442772
        0.6%
        44.7%
        96.4%
        1.2%
        ERR1442773
        0.4%
        45.1%
        96.6%
        1.6%
        ERR1442774
        0.5%
        44.8%
        96.5%
        1.5%
        ERR1442775
        0.5%
        44.9%
        96.5%
        1.6%
        ERR1442776
        0.5%
        44.9%
        96.2%
        1.3%
        ERR1442777
        0.4%
        44.9%
        96.5%
        1.5%
        ERR1442778
        0.5%
        44.9%
        96.6%
        1.4%
        ERR1442779
        0.5%
        44.9%
        96.4%
        1.2%
        ERR1442780
        0.5%
        44.6%
        96.5%
        1.4%
        ERR1442791
        0.4%
        45.0%
        96.2%
        2.1%
        ERR1442792
        0.6%
        45.0%
        96.0%
        2.0%
        ERR1442793
        0.6%
        44.8%
        96.1%
        1.9%
        ERR1442794
        0.5%
        45.4%
        96.3%
        1.9%
        ERR1442795
        0.5%
        45.2%
        96.2%
        1.5%
        ERR1442796
        0.7%
        45.4%
        95.7%
        1.4%
        ERR1442797
        0.7%
        45.1%
        96.2%
        2.5%
        ERR1442798
        0.5%
        45.4%
        96.4%
        1.7%
        ERR1442799
        0.4%
        45.8%
        96.4%
        1.6%
        ERR1442800
        0.4%
        45.6%
        96.5%
        1.7%
        ERR1442820
        0.4%
        45.4%
        96.4%
        1.8%
        ERR1442836
        0.7%
        45.1%
        95.8%
        1.5%
        ERR1442837
        0.5%
        45.4%
        96.1%
        1.7%
        ERR1442838
        0.6%
        45.4%
        96.7%
        2.4%
        ERR1442839
        0.6%
        45.6%
        96.5%
        2.7%
        ERR1442840
        0.6%
        45.4%
        95.9%
        1.5%
        ERR1442841
        0.4%
        45.6%
        96.2%
        1.6%
        ERR1442842
        0.7%
        45.3%
        95.6%
        1.6%
        ERR1442843
        0.5%
        45.9%
        96.2%
        1.4%
        ERR1442844
        0.5%
        45.8%
        96.2%
        1.4%
        ERR1442845
        0.5%
        45.8%
        96.3%
        1.4%
        ERR1442846
        0.6%
        45.0%
        96.4%
        1.7%
        ERR1442847
        0.4%
        45.8%
        96.6%
        2.0%
        ERR1442848
        0.5%
        45.3%
        96.2%
        1.7%
        ERR1442849
        0.5%
        45.3%
        96.1%
        1.7%
        ERR1442850
        0.5%
        45.4%
        96.0%
        1.9%
        ERR1442851
        0.5%
        45.3%
        96.3%
        1.7%
        ERR1442852
        0.5%
        45.2%
        96.3%
        1.4%
        ERR1442853
        0.6%
        45.4%
        96.2%
        1.5%
        ERR1442854
        0.6%
        45.0%
        96.1%
        1.7%
        ERR1442855
        0.4%
        46.0%
        96.5%
        1.9%
        ERR1442856
        0.5%
        44.6%
        96.2%
        1.5%
        ERR1442857
        0.4%
        44.9%
        96.3%
        1.5%
        ERR1442858
        0.5%
        44.6%
        96.2%
        1.3%
        ERR1442859
        0.5%
        44.7%
        96.4%
        1.5%
        ERR1442860
        0.7%
        44.2%
        95.8%
        1.4%
        ERR1442861
        0.5%
        44.9%
        96.3%
        1.3%
        ERR1442862
        0.5%
        44.7%
        96.3%
        1.2%
        ERR1442863
        0.4%
        45.1%
        96.5%
        1.6%
        ERR1442864
        0.4%
        44.8%
        96.4%
        1.5%
        ERR1442865
        0.5%
        44.9%
        96.4%
        1.6%
        ERR1442866
        0.5%
        44.9%
        96.1%
        1.3%
        ERR1442867
        0.4%
        44.9%
        96.4%
        1.5%
        ERR1442868
        0.5%
        44.9%
        96.4%
        1.4%
        ERR1442869
        0.5%
        44.9%
        96.2%
        1.2%
        ERR1442870
        0.5%
        44.6%
        96.3%
        1.4%
        ERR1442881
        0.4%
        45.0%
        96.0%
        2.1%
        ERR1442882
        0.5%
        45.0%
        95.9%
        2.0%
        ERR1442883
        0.6%
        44.8%
        95.9%
        1.9%
        ERR1442884
        0.5%
        45.4%
        96.2%
        1.9%
        ERR1442885
        0.5%
        45.2%
        96.1%
        1.5%
        ERR1442886
        0.7%
        45.3%
        95.6%
        1.4%
        ERR1442887
        0.7%
        45.1%
        96.0%
        2.5%
        ERR1442888
        0.4%
        45.3%
        96.3%
        1.7%
        ERR1442889
        0.4%
        45.8%
        96.2%
        1.5%
        ERR1442890
        0.4%
        45.5%
        96.3%
        1.7%
        ERR1442910
        0.4%
        45.4%
        96.3%
        1.8%
        Long-pec-1
        1.3%
        45.2%
        100.0%
        0.0%
        237 bp
        6.9%
        100.0%
        10.3
        0.8 X
        11.2
        0.4
        Long-pec-2
        1.5%
        45.2%
        100.0%
        0.0%
        240 bp
        7.2%
        100.0%
        10.0
        0.8 X
        11.1
        0.4
        Long-pec-3
        1.6%
        45.4%
        100.0%
        0.0%
        242 bp
        7.6%
        100.0%
        11.2
        0.9 X
        12.4
        0.4
        Long-pec-4
        1.7%
        45.0%
        100.0%
        0.0%
        236 bp
        8.1%
        100.0%
        11.6
        1.0 X
        13.2
        0.5
        Long-pec-5
        1.5%
        46.0%
        100.0%
        0.0%
        224 bp
        8.2%
        100.0%
        12.2
        1.0 X
        13.1
        0.5
        Prim-15-1
        1.3%
        45.6%
        100.0%
        0.0%
        239 bp
        6.3%
        100.0%
        10.0
        0.8 X
        11.0
        0.4
        Prim-15-2
        1.9%
        45.3%
        100.0%
        0.0%
        232 bp
        9.0%
        100.0%
        10.7
        0.9 X
        12.6
        0.4
        Prim-15-3
        1.4%
        45.8%
        100.0%
        0.0%
        248 bp
        6.5%
        100.0%
        9.9
        0.8 X
        11.1
        0.4
        Prim-15-4
        1.4%
        45.8%
        100.0%
        0.0%
        245 bp
        6.5%
        100.0%
        10.1
        0.8 X
        11.3
        0.4
        Prim-15-5
        1.5%
        45.8%
        100.0%
        0.0%
        242 bp
        7.0%
        100.0%
        11.4
        0.9 X
        12.6
        0.5
        Prim-25-1
        1.6%
        45.0%
        100.0%
        0.0%
        218 bp
        7.3%
        100.0%
        11.6
        1.0 X
        13.4
        0.5
        Prim-25-2
        1.4%
        45.8%
        100.0%
        0.0%
        225 bp
        6.9%
        100.0%
        13.2
        1.0 X
        14.4
        0.5
        Prim-25-3
        1.4%
        45.3%
        100.0%
        0.0%
        230 bp
        6.7%
        100.0%
        10.8
        0.9 X
        12.1
        0.5
        Prim-25-4
        1.4%
        45.3%
        100.0%
        0.0%
        234 bp
        6.8%
        100.0%
        10.9
        0.9 X
        12.1
        0.5
        Prim-25-5
        1.4%
        45.4%
        100.0%
        0.0%
        231 bp
        6.8%
        100.0%
        10.2
        0.8 X
        11.5
        0.5
        Prim-5-1
        1.7%
        45.1%
        100.0%
        0.0%
        248 bp
        6.6%
        100.0%
        10.2
        0.8 X
        11.6
        0.4
        Prim-5-2
        1.5%
        45.4%
        100.0%
        0.0%
        240 bp
        6.5%
        100.0%
        9.7
        0.8 X
        11.1
        0.4
        Prim-5-3
        1.9%
        45.4%
        100.0%
        0.0%
        207 bp
        8.0%
        100.0%
        14.1
        1.2 X
        16.1
        0.6
        Prim-5-4
        1.8%
        45.6%
        100.0%
        0.0%
        207 bp
        8.1%
        100.0%
        13.8
        1.1 X
        15.7
        0.5
        Prim-5-5
        1.4%
        45.4%
        100.0%
        0.0%
        244 bp
        6.4%
        100.0%
        9.6
        0.8 X
        11.0
        0.4
        Protruding-mouth-1
        1.6%
        44.6%
        100.0%
        0.0%
        233 bp
        6.8%
        100.0%
        11.3
        0.9 X
        12.5
        0.5
        Protruding-mouth-2
        1.3%
        44.9%
        100.0%
        0.0%
        240 bp
        6.0%
        100.0%
        10.5
        0.8 X
        11.3
        0.5
        Protruding-mouth-3
        1.5%
        44.6%
        100.0%
        0.0%
        239 bp
        6.7%
        100.0%
        12.0
        1.0 X
        13.1
        0.6
        Protruding-mouth-4
        1.5%
        44.7%
        100.0%
        0.0%
        233 bp
        6.5%
        100.0%
        11.7
        0.9 X
        12.8
        0.5
        Protruding-mouth-5
        1.8%
        44.2%
        100.0%
        0.0%
        232 bp
        7.6%
        100.0%
        11.5
        0.9 X
        12.9
        0.5

        Workflow explanation

        Oh no! Something went wrong... Please let us know: https://github.com/vanheeringen-lab/seq2science/issues

        Assembly stats

        Genome assembly GRCz11 contains of 993 contigs, with a GC-content of 36.65%, and 0.34% consists of the letter N. The N50-L50 stats are 54304671-11 and the N75-L75 stats are 48040578-18. The genome annotation contains 30954 genes.

        fastp

        fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)

        Filtered Reads

        Filtering statistics of sampled reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Duplication Rates

        Duplication rates of sampled reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Insert Sizes

        Insert size estimation of sampled reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        GC Content

        Average GC content over each base of all reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        N content

        Average N content over each base of all reads.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).

        Picard

        Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

        Insert Size

        Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

        loading..

        Mark Duplicates

        Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

        The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

        To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

        • READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
        • READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
        • READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
        • READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
        • READS_UNMAPPED = UNMAPPED_READS
        loading..

        SamTools pre-sieve

        Samtools is a suite of programs for interacting with high-throughput sequencing data.

        The pre-sieve statistics are quality metrics measured before applying (optional) minimum mapping quality, blacklist removal, mitochondrial read removal, read length filtering, and tn5 shift.

        Percent Mapped

        Alignment metrics from samtools stats; mapped vs. unmapped reads.

        For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

        Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

        loading..

        Alignment metrics

        This module parses the output from samtools stats. All numbers in millions.

        loading..

        deepTools

        deepTools is a suite of tools to process and analyze deep sequencing data.

        PCA plot

        PCA plot with the top two principal components calculated based on genome-wide distribution of sequence reads

        loading..

        Fingerprint plot

        Signal fingerprint according to plotFingerprint

        loading..

        Strandedness

        Strandedness package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

        Sequencing strandedness was inferred for the following samples, and was called if 60% of the sampled reads were explained by either sense (forward) or antisense (reverse).

        Infer experiment

        Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

        loading..

        deepTools - Spearman correlation heatmap of reads in bins across the genome

        Spearman correlation plot generated by deeptools. Spearman correlation is a non-parametric (distribution-free) method, and assesses the monotonicity of the relationship.

        deepTools - Pearson correlation heatmap of reads in bins across the genome

        Pearson correlation plot generated by deeptools. Pearson correlation is a parametric (lots of assumptions, e.g. normality and homoscedasticity) method, and assesses the linearity of the relationship.

        dupRadar

        Figures generated by [dupRadar](https://bioconductor.riken.jp/packages/3.4/bioc/vignettes/dupRadar/inst/doc/dupRadar.html#plotting-and-interpretation). Click the link for help with interpretation.

        DESeq2 - Sample distance cluster heatmap of counts

        Euclidean distance between samples, based on variance stabilizing transformed counts (RNA: expressed genes, ChIP: bound regions, ATAC: accessible regions). Gives us an overview of similarities and dissimilarities between samples.

        DESeq2 - Spearman correlation cluster heatmap of counts

        Correlation cluster heatmap based on variance stabilizing transformed counts. Spearman correlation is a non-parametric (distribution-free) method, and assesses the monotonicity of the relationship.

        DESeq2 - Pearson correlation cluster heatmap of counts

        Correlation cluster heatmap based on variance stabilizing transformed counts. Pearson correlation is a parametric (lots of assumptions, e.g. normality and homoscedasticity) method, and assesses the linearity of the relationship.

        Samples & Config

        The samples file used for this run:

        sample assembly stage technical_replicates descriptive_name
        ERR1442640 GRCz11 1-4-somites 1-4-somites-5 10.33hpf_D177
        ERR1442730 GRCz11 1-4-somites 1-4-somites-5 10.33hpf_D178
        ERR1442820 GRCz11 1-4-somites 1-4-somites-5 10.33hpf_D179
        ERR1442910 GRCz11 1-4-somites 1-4-somites-5 10.33hpf_D180
        ERR1442611 GRCz11 14-19-somites 14-19-somites-1 16hpf_D181
        ERR1442701 GRCz11 14-19-somites 14-19-somites-1 16hpf_D182
        ERR1442791 GRCz11 14-19-somites 14-19-somites-1 16hpf_D183
        ERR1442881 GRCz11 14-19-somites 14-19-somites-1 16hpf_D184
        ERR1442612 GRCz11 14-19-somites 14-19-somites-2 16hpf_D185
        ERR1442702 GRCz11 14-19-somites 14-19-somites-2 16hpf_D186
        ERR1442792 GRCz11 14-19-somites 14-19-somites-2 16hpf_D187
        ERR1442882 GRCz11 14-19-somites 14-19-somites-2 16hpf_D188
        ERR1442613 GRCz11 14-19-somites 14-19-somites-3 16hpf_D189
        ERR1442703 GRCz11 14-19-somites 14-19-somites-3 16hpf_D190
        ERR1442793 GRCz11 14-19-somites 14-19-somites-3 16hpf_D191
        ERR1442883 GRCz11 14-19-somites 14-19-somites-3 16hpf_D192
        ERR1442614 GRCz11 14-19-somites 14-19-somites-4 16hpf_D193
        ERR1442704 GRCz11 14-19-somites 14-19-somites-4 16hpf_D194
        ERR1442794 GRCz11 14-19-somites 14-19-somites-4 16hpf_D195
        ERR1442884 GRCz11 14-19-somites 14-19-somites-4 16hpf_D196
        ERR1442615 GRCz11 14-19-somites 14-19-somites-5 16hpf_D197
        ERR1442705 GRCz11 14-19-somites 14-19-somites-5 16hpf_D198
        ERR1442795 GRCz11 14-19-somites 14-19-somites-5 16hpf_D199
        ERR1442885 GRCz11 14-19-somites 14-19-somites-5 16hpf_D200
        ERR1442616 GRCz11 20-25-somites 20-25-somites-1 19hpf_D201
        ERR1442706 GRCz11 20-25-somites 20-25-somites-1 19hpf_D202
        ERR1442796 GRCz11 20-25-somites 20-25-somites-1 19hpf_D203
        ERR1442886 GRCz11 20-25-somites 20-25-somites-1 19hpf_D204
        ERR1442617 GRCz11 20-25-somites 20-25-somites-2 19hpf_D205
        ERR1442707 GRCz11 20-25-somites 20-25-somites-2 19hpf_D206
        ERR1442797 GRCz11 20-25-somites 20-25-somites-2 19hpf_D207
        ERR1442887 GRCz11 20-25-somites 20-25-somites-2 19hpf_D208
        ERR1442618 GRCz11 20-25-somites 20-25-somites-3 19hpf_D209
        ERR1442708 GRCz11 20-25-somites 20-25-somites-3 19hpf_D210
        ERR1442798 GRCz11 20-25-somites 20-25-somites-3 19hpf_D211
        ERR1442888 GRCz11 20-25-somites 20-25-somites-3 19hpf_D212
        ERR1442619 GRCz11 20-25-somites 20-25-somites-4 19hpf_D213
        ERR1442709 GRCz11 20-25-somites 20-25-somites-4 19hpf_D214
        ERR1442799 GRCz11 20-25-somites 20-25-somites-4 19hpf_D215
        ERR1442889 GRCz11 20-25-somites 20-25-somites-4 19hpf_D216
        ERR1442620 GRCz11 20-25-somites 20-25-somites-5 19hpf_D217
        ERR1442710 GRCz11 20-25-somites 20-25-somites-5 19hpf_D218
        ERR1442800 GRCz11 20-25-somites 20-25-somites-5 19hpf_D219
        ERR1442890 GRCz11 20-25-somites 20-25-somites-5 19hpf_D220
        ERR1442566 GRCz11 Prim-5 Prim-5-1 24hpf_D221
        ERR1442656 GRCz11 Prim-5 Prim-5-1 24hpf_D222
        ERR1442746 GRCz11 Prim-5 Prim-5-1 24hpf_D223
        ERR1442836 GRCz11 Prim-5 Prim-5-1 24hpf_D224
        ERR1442567 GRCz11 Prim-5 Prim-5-2 24hpf_D225
        ERR1442657 GRCz11 Prim-5 Prim-5-2 24hpf_D226
        ERR1442747 GRCz11 Prim-5 Prim-5-2 24hpf_D227
        ERR1442837 GRCz11 Prim-5 Prim-5-2 24hpf_D228
        ERR1442568 GRCz11 Prim-5 Prim-5-3 24hpf_D229
        ERR1442658 GRCz11 Prim-5 Prim-5-3 24hpf_D230
        ERR1442748 GRCz11 Prim-5 Prim-5-3 24hpf_D231
        ERR1442838 GRCz11 Prim-5 Prim-5-3 24hpf_D232
        ERR1442569 GRCz11 Prim-5 Prim-5-4 24hpf_D233
        ERR1442659 GRCz11 Prim-5 Prim-5-4 24hpf_D234
        ERR1442749 GRCz11 Prim-5 Prim-5-4 24hpf_D235
        ERR1442839 GRCz11 Prim-5 Prim-5-4 24hpf_D236
        ERR1442570 GRCz11 Prim-5 Prim-5-5 24hpf_D237
        ERR1442660 GRCz11 Prim-5 Prim-5-5 24hpf_D238
        ERR1442750 GRCz11 Prim-5 Prim-5-5 24hpf_D239
        ERR1442840 GRCz11 Prim-5 Prim-5-5 24hpf_D240
        ERR1442571 GRCz11 Prim-15 Prim-15-1 30hpf_D241
        ERR1442661 GRCz11 Prim-15 Prim-15-1 30hpf_D242
        ERR1442751 GRCz11 Prim-15 Prim-15-1 30hpf_D243
        ERR1442841 GRCz11 Prim-15 Prim-15-1 30hpf_D244
        ERR1442572 GRCz11 Prim-15 Prim-15-2 30hpf_D245
        ERR1442662 GRCz11 Prim-15 Prim-15-2 30hpf_D246
        ERR1442752 GRCz11 Prim-15 Prim-15-2 30hpf_D247
        ERR1442842 GRCz11 Prim-15 Prim-15-2 30hpf_D248
        ERR1442573 GRCz11 Prim-15 Prim-15-3 30hpf_D249
        ERR1442663 GRCz11 Prim-15 Prim-15-3 30hpf_D250
        ERR1442753 GRCz11 Prim-15 Prim-15-3 30hpf_D251
        ERR1442843 GRCz11 Prim-15 Prim-15-3 30hpf_D252
        ERR1442574 GRCz11 Prim-15 Prim-15-4 30hpf_D253
        ERR1442664 GRCz11 Prim-15 Prim-15-4 30hpf_D254
        ERR1442754 GRCz11 Prim-15 Prim-15-4 30hpf_D255
        ERR1442844 GRCz11 Prim-15 Prim-15-4 30hpf_D256
        ERR1442575 GRCz11 Prim-15 Prim-15-5 30hpf_D257
        ERR1442665 GRCz11 Prim-15 Prim-15-5 30hpf_D258
        ERR1442755 GRCz11 Prim-15 Prim-15-5 30hpf_D259
        ERR1442845 GRCz11 Prim-15 Prim-15-5 30hpf_D260
        ERR1442576 GRCz11 Prim-25 Prim-25-1 36hpf_D261
        ERR1442666 GRCz11 Prim-25 Prim-25-1 36hpf_D262
        ERR1442756 GRCz11 Prim-25 Prim-25-1 36hpf_D263
        ERR1442846 GRCz11 Prim-25 Prim-25-1 36hpf_D264
        ERR1442577 GRCz11 Prim-25 Prim-25-2 36hpf_D265
        ERR1442667 GRCz11 Prim-25 Prim-25-2 36hpf_D266
        ERR1442757 GRCz11 Prim-25 Prim-25-2 36hpf_D267
        ERR1442847 GRCz11 Prim-25 Prim-25-2 36hpf_D268
        ERR1442578 GRCz11 Prim-25 Prim-25-3 36hpf_D269
        ERR1442668 GRCz11 Prim-25 Prim-25-3 36hpf_D270
        ERR1442758 GRCz11 Prim-25 Prim-25-3 36hpf_D271
        ERR1442848 GRCz11 Prim-25 Prim-25-3 36hpf_D272
        ERR1442579 GRCz11 Prim-25 Prim-25-4 36hpf_D273
        ERR1442669 GRCz11 Prim-25 Prim-25-4 36hpf_D274
        ERR1442759 GRCz11 Prim-25 Prim-25-4 36hpf_D275
        ERR1442849 GRCz11 Prim-25 Prim-25-4 36hpf_D276
        ERR1442580 GRCz11 Prim-25 Prim-25-5 36hpf_D277
        ERR1442670 GRCz11 Prim-25 Prim-25-5 36hpf_D278
        ERR1442760 GRCz11 Prim-25 Prim-25-5 36hpf_D279
        ERR1442850 GRCz11 Prim-25 Prim-25-5 36hpf_D280
        ERR1442581 GRCz11 Long-pec Long-pec-1 48hpf_D281
        ERR1442671 GRCz11 Long-pec Long-pec-1 48hpf_D282
        ERR1442761 GRCz11 Long-pec Long-pec-1 48hpf_D283
        ERR1442851 GRCz11 Long-pec Long-pec-1 48hpf_D284
        ERR1442582 GRCz11 Long-pec Long-pec-2 48hpf_D285
        ERR1442672 GRCz11 Long-pec Long-pec-2 48hpf_D286
        ERR1442762 GRCz11 Long-pec Long-pec-2 48hpf_D287
        ERR1442852 GRCz11 Long-pec Long-pec-2 48hpf_D288
        ERR1442583 GRCz11 Long-pec Long-pec-3 48hpf_D289
        ERR1442673 GRCz11 Long-pec Long-pec-3 48hpf_D290
        ERR1442763 GRCz11 Long-pec Long-pec-3 48hpf_D291
        ERR1442853 GRCz11 Long-pec Long-pec-3 48hpf_D292
        ERR1442584 GRCz11 Long-pec Long-pec-4 48hpf_D293
        ERR1442674 GRCz11 Long-pec Long-pec-4 48hpf_D294
        ERR1442764 GRCz11 Long-pec Long-pec-4 48hpf_D295
        ERR1442854 GRCz11 Long-pec Long-pec-4 48hpf_D296
        ERR1442585 GRCz11 Long-pec Long-pec-5 48hpf_D297
        ERR1442675 GRCz11 Long-pec Long-pec-5 48hpf_D298
        ERR1442765 GRCz11 Long-pec Long-pec-5 48hpf_D299
        ERR1442855 GRCz11 Long-pec Long-pec-5 48hpf_D300
        ERR1442586 GRCz11 Protruding-mouth Protruding-mouth-1 72hpf_D301
        ERR1442676 GRCz11 Protruding-mouth Protruding-mouth-1 72hpf_D302
        ERR1442766 GRCz11 Protruding-mouth Protruding-mouth-1 72hpf_D303
        ERR1442856 GRCz11 Protruding-mouth Protruding-mouth-1 72hpf_D304
        ERR1442587 GRCz11 Protruding-mouth Protruding-mouth-2 72hpf_D305
        ERR1442677 GRCz11 Protruding-mouth Protruding-mouth-2 72hpf_D306
        ERR1442767 GRCz11 Protruding-mouth Protruding-mouth-2 72hpf_D307
        ERR1442857 GRCz11 Protruding-mouth Protruding-mouth-2 72hpf_D308
        ERR1442588 GRCz11 Protruding-mouth Protruding-mouth-3 72hpf_D309
        ERR1442678 GRCz11 Protruding-mouth Protruding-mouth-3 72hpf_D310
        ERR1442768 GRCz11 Protruding-mouth Protruding-mouth-3 72hpf_D311
        ERR1442858 GRCz11 Protruding-mouth Protruding-mouth-3 72hpf_D312
        ERR1442589 GRCz11 Protruding-mouth Protruding-mouth-4 72hpf_D313
        ERR1442679 GRCz11 Protruding-mouth Protruding-mouth-4 72hpf_D314
        ERR1442769 GRCz11 Protruding-mouth Protruding-mouth-4 72hpf_D315
        ERR1442859 GRCz11 Protruding-mouth Protruding-mouth-4 72hpf_D316
        ERR1442590 GRCz11 Protruding-mouth Protruding-mouth-5 72hpf_D317
        ERR1442680 GRCz11 Protruding-mouth Protruding-mouth-5 72hpf_D318
        ERR1442770 GRCz11 Protruding-mouth Protruding-mouth-5 72hpf_D319
        ERR1442860 GRCz11 Protruding-mouth Protruding-mouth-5 72hpf_D320
        ERR1442591 GRCz11 Day-4 Day-4-1 96hpf_D321
        ERR1442681 GRCz11 Day-4 Day-4-1 96hpf_D322
        ERR1442771 GRCz11 Day-4 Day-4-1 96hpf_D323
        ERR1442861 GRCz11 Day-4 Day-4-1 96hpf_D324
        ERR1442592 GRCz11 Day-4 Day-4-2 96hpf_D325
        ERR1442682 GRCz11 Day-4 Day-4-2 96hpf_D326
        ERR1442772 GRCz11 Day-4 Day-4-2 96hpf_D327
        ERR1442862 GRCz11 Day-4 Day-4-2 96hpf_D328
        ERR1442593 GRCz11 Day-4 Day-4-3 96hpf_D329
        ERR1442683 GRCz11 Day-4 Day-4-3 96hpf_D330
        ERR1442773 GRCz11 Day-4 Day-4-3 96hpf_D331
        ERR1442863 GRCz11 Day-4 Day-4-3 96hpf_D332
        ERR1442594 GRCz11 Day-4 Day-4-4 96hpf_D333
        ERR1442684 GRCz11 Day-4 Day-4-4 96hpf_D334
        ERR1442774 GRCz11 Day-4 Day-4-4 96hpf_D335
        ERR1442864 GRCz11 Day-4 Day-4-4 96hpf_D336
        ERR1442595 GRCz11 Day-4 Day-4-5 96hpf_D337
        ERR1442685 GRCz11 Day-4 Day-4-5 96hpf_D338
        ERR1442775 GRCz11 Day-4 Day-4-5 96hpf_D339
        ERR1442865 GRCz11 Day-4 Day-4-5 96hpf_D340
        ERR1442596 GRCz11 Day-5 Day-5-1 120hpf_D341
        ERR1442686 GRCz11 Day-5 Day-5-1 120hpf_D342
        ERR1442776 GRCz11 Day-5 Day-5-1 120hpf_D343
        ERR1442866 GRCz11 Day-5 Day-5-1 120hpf_D344
        ERR1442597 GRCz11 Day-5 Day-5-2 120hpf_D345
        ERR1442687 GRCz11 Day-5 Day-5-2 120hpf_D346
        ERR1442777 GRCz11 Day-5 Day-5-2 120hpf_D347
        ERR1442867 GRCz11 Day-5 Day-5-2 120hpf_D348
        ERR1442598 GRCz11 Day-5 Day-5-3 120hpf_D349
        ERR1442688 GRCz11 Day-5 Day-5-3 120hpf_D350
        ERR1442778 GRCz11 Day-5 Day-5-3 120hpf_D351
        ERR1442868 GRCz11 Day-5 Day-5-3 120hpf_D352
        ERR1442599 GRCz11 Day-5 Day-5-4 120hpf_D353
        ERR1442689 GRCz11 Day-5 Day-5-4 120hpf_D354
        ERR1442779 GRCz11 Day-5 Day-5-4 120hpf_D355
        ERR1442869 GRCz11 Day-5 Day-5-4 120hpf_D356
        ERR1442600 GRCz11 Day-5 Day-5-5 120hpf_D357
        ERR1442690 GRCz11 Day-5 Day-5-5 120hpf_D358
        ERR1442780 GRCz11 Day-5 Day-5-5 120hpf_D359
        ERR1442870 GRCz11 Day-5 Day-5-5 120hpf_D360

        The config file used for this run: 
        # tab-separated file of the samples
samples: samples_pt5.tsv

# pipeline file locations
result_dir: /bank/tdewijs/results_Dre/pt5  # where to store results
genome_dir: /bank/tdewijs/genomes  # where to look for or download the genomes
fastq_dir: /bank/tdewijs/fastq  # where to look for or download the fastqs


# contact info for multiqc report and trackhub
email: tessa.dewijs2@ru.nl

# produce a UCSC trackhub?
create_trackhub: true

# how to handle replicates
technical_replicates: merge    # change to "keep" to not combine them

# which trimmer to use
trimmer: fastp

# which quantifier to use
quantifier: salmon  # or salmon or featurecounts

# which aligner to use (not used for the gene counts matrix if the quantifier is Salmon)
aligner: star

# filtering after alignment (not used for the gene counts matrix if the quantifier is Salmon)
remove_blacklist: true
min_mapping_quality: 255  # (only keep uniquely mapped reads from STAR alignments)
only_primary_align: true
remove_dups: false # keep duplicates (check dupRadar in the MultiQC)

## differential gene expression analysis
#contrasts:
#  - 'stage_2_1'

        MultiQC v1.11 - Written by Phil Ewels, available on GitHub.

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