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 11, 2022
        Project
        pt4
        Contact E-mail
        tessa.dewijs2@ru.nl

        Report generated on 2022-01-11, 23:52 based on data in:

        Change sample names:

        Show/Hide samples:

        General Statistics

        Showing 225/225 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-1
        1.5%
        46.2%
        100.0%
        0.0%
        209 bp
        7.7%
        100.0%
        13.0
        1.1 X
        15.0
        0.6
        1-4-somites-2
        1.6%
        45.2%
        100.0%
        0.0%
        237 bp
        7.0%
        100.0%
        11.0
        0.9 X
        12.9
        0.6
        1-4-somites-3
        1.3%
        46.6%
        100.0%
        0.0%
        232 bp
        6.9%
        100.0%
        10.6
        0.9 X
        12.3
        0.5
        1-4-somites-4
        1.4%
        45.8%
        100.0%
        0.0%
        224 bp
        7.2%
        100.0%
        13.4
        1.1 X
        15.1
        0.7
        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
        1-cell-1
        2.2%
        48.3%
        100.0%
        0.0%
        218 bp
        9.6%
        100.0%
        10.6
        0.7 X
        10.2
        1.0
        1-cell-2
        2.1%
        47.8%
        100.0%
        0.0%
        229 bp
        9.0%
        100.0%
        9.2
        0.6 X
        8.9
        0.9
        1-cell-3
        2.5%
        47.4%
        100.0%
        0.0%
        212 bp
        9.7%
        100.0%
        9.9
        0.7 X
        9.6
        0.9
        1-cell-4
        2.8%
        47.1%
        100.0%
        0.0%
        185 bp
        10.2%
        100.0%
        10.1
        0.7 X
        9.8
        0.9
        1-cell-5
        2.6%
        46.5%
        100.0%
        0.0%
        183 bp
        9.8%
        100.0%
        8.0
        0.6 X
        7.7
        0.8
        128-cell-1
        1.6%
        48.7%
        100.0%
        0.0%
        250 bp
        5.7%
        100.0%
        12.1
        0.9 X
        12.5
        0.6
        128-cell-2
        1.5%
        47.1%
        100.0%
        0.0%
        248 bp
        5.0%
        100.0%
        11.0
        0.8 X
        11.3
        0.5
        128-cell-3
        1.8%
        48.2%
        100.0%
        0.0%
        220 bp
        5.7%
        100.0%
        13.2
        1.0 X
        13.5
        0.6
        128-cell-4
        1.9%
        48.0%
        100.0%
        0.0%
        210 bp
        6.7%
        100.0%
        11.3
        0.9 X
        12.0
        0.5
        128-cell-5
        1.4%
        47.4%
        100.0%
        0.0%
        235 bp
        5.2%
        100.0%
        11.2
        0.8 X
        11.4
        0.6
        1k-cell-1
        2.0%
        46.7%
        100.0%
        0.0%
        173 bp
        6.5%
        100.0%
        14.3
        1.1 X
        15.0
        0.7
        1k-cell-2
        1.7%
        47.7%
        100.0%
        0.0%
        184 bp
        5.9%
        100.0%
        14.4
        1.1 X
        14.8
        0.6
        1k-cell-3
        1.4%
        47.4%
        100.0%
        0.0%
        222 bp
        5.7%
        100.0%
        10.7
        0.8 X
        11.0
        0.6
        1k-cell-4
        1.5%
        47.2%
        100.0%
        0.0%
        235 bp
        5.2%
        100.0%
        11.3
        0.8 X
        11.6
        0.6
        1k-cell-5
        1.4%
        47.4%
        100.0%
        0.0%
        231 bp
        5.1%
        100.0%
        11.0
        0.8 X
        11.3
        0.6
        2-cell-1
        2.6%
        47.3%
        100.0%
        0.0%
        228 bp
        8.8%
        100.0%
        10.0
        0.7 X
        9.7
        0.9
        2-cell-2
        2.2%
        46.8%
        100.0%
        0.0%
        227 bp
        8.3%
        100.0%
        10.2
        0.7 X
        10.0
        0.9
        2-cell-3
        2.3%
        47.2%
        100.0%
        0.0%
        228 bp
        8.0%
        100.0%
        10.4
        0.7 X
        10.1
        0.9
        2-cell-4
        2.1%
        47.8%
        100.0%
        0.0%
        239 bp
        7.6%
        100.0%
        9.9
        0.7 X
        9.7
        0.8
        2-cell-5
        2.1%
        47.5%
        100.0%
        0.0%
        214 bp
        8.5%
        100.0%
        11.3
        0.8 X
        10.9
        1.0
        50pc-epiboly-1
        1.8%
        45.7%
        100.0%
        0.0%
        194 bp
        7.5%
        100.0%
        11.3
        0.9 X
        12.3
        0.8
        50pc-epiboly-2
        2.0%
        45.3%
        100.0%
        0.0%
        194 bp
        7.8%
        100.0%
        11.3
        0.9 X
        12.8
        0.7
        50pc-epiboly-3
        1.9%
        46.1%
        100.0%
        0.0%
        225 bp
        7.4%
        100.0%
        11.6
        0.9 X
        12.6
        0.8
        50pc-epiboly-4
        1.6%
        45.9%
        100.0%
        0.0%
        228 bp
        6.6%
        100.0%
        10.6
        0.8 X
        11.5
        0.7
        50pc-epiboly-5
        1.5%
        45.7%
        100.0%
        0.0%
        226 bp
        6.6%
        100.0%
        9.8
        0.8 X
        10.5
        0.7
        75pc-epiboly-1
        1.5%
        46.8%
        100.0%
        0.0%
        234 bp
        7.1%
        100.0%
        11.2
        0.9 X
        12.6
        0.6
        75pc-epiboly-2
        1.5%
        46.4%
        100.0%
        0.0%
        240 bp
        6.9%
        100.0%
        11.3
        0.9 X
        12.7
        0.6
        75pc-epiboly-3
        2.3%
        45.0%
        100.0%
        0.0%
        227 bp
        9.7%
        100.0%
        11.3
        0.9 X
        13.0
        0.6
        75pc-epiboly-4
        1.8%
        47.1%
        100.0%
        0.0%
        223 bp
        8.5%
        100.0%
        11.2
        0.9 X
        12.7
        0.6
        75pc-epiboly-5
        1.4%
        46.3%
        100.0%
        0.0%
        238 bp
        6.6%
        100.0%
        10.3
        0.8 X
        11.5
        0.5
        Dome-1
        1.8%
        46.0%
        100.0%
        0.0%
        229 bp
        7.0%
        100.0%
        10.9
        0.8 X
        11.5
        0.9
        Dome-2
        1.9%
        46.7%
        100.0%
        0.0%
        224 bp
        6.9%
        100.0%
        11.9
        0.9 X
        12.5
        0.9
        Dome-3
        2.1%
        45.7%
        100.0%
        0.0%
        217 bp
        8.0%
        100.0%
        11.2
        0.9 X
        11.9
        0.9
        Dome-4
        1.6%
        46.5%
        100.0%
        0.0%
        230 bp
        6.0%
        100.0%
        10.8
        0.8 X
        11.2
        0.8
        Dome-5
        2.0%
        47.3%
        100.0%
        0.0%
        219 bp
        6.1%
        100.0%
        10.8
        0.8 X
        11.2
        0.7
        ERR1442561
        0.5%
        45.7%
        97.3%
        3.1%
        ERR1442562
        0.6%
        45.3%
        97.2%
        3.0%
        ERR1442563
        0.4%
        46.1%
        97.1%
        1.9%
        ERR1442564
        0.4%
        45.9%
        97.1%
        1.8%
        ERR1442565
        0.4%
        45.7%
        97.0%
        2.1%
        ERR1442601
        0.4%
        47.2%
        97.0%
        1.8%
        ERR1442602
        0.3%
        46.8%
        97.3%
        1.8%
        ERR1442603
        0.4%
        46.9%
        97.2%
        1.7%
        ERR1442604
        0.4%
        46.8%
        97.1%
        1.7%
        ERR1442605
        0.5%
        46.0%
        96.9%
        1.8%
        ERR1442606
        0.4%
        46.8%
        97.3%
        1.7%
        ERR1442607
        0.4%
        46.4%
        97.1%
        1.3%
        ERR1442608
        0.6%
        45.0%
        95.5%
        1.5%
        ERR1442609
        0.4%
        47.1%
        97.1%
        2.1%
        ERR1442610
        0.4%
        46.3%
        96.9%
        1.8%
        ERR1442621
        0.4%
        46.0%
        96.9%
        1.5%
        ERR1442622
        0.4%
        46.7%
        96.9%
        1.8%
        ERR1442623
        0.5%
        45.7%
        96.5%
        1.7%
        ERR1442624
        0.4%
        46.5%
        97.3%
        1.7%
        ERR1442625
        0.4%
        47.3%
        97.6%
        2.4%
        ERR1442626
        0.5%
        47.3%
        97.0%
        2.1%
        ERR1442627
        0.5%
        46.8%
        97.0%
        1.9%
        ERR1442628
        0.5%
        47.2%
        97.0%
        1.9%
        ERR1442629
        0.4%
        47.8%
        97.2%
        1.8%
        ERR1442630
        0.5%
        47.5%
        97.4%
        2.5%
        ERR1442631
        0.3%
        48.7%
        97.5%
        1.6%
        ERR1442632
        0.4%
        47.2%
        96.9%
        1.6%
        ERR1442633
        0.4%
        48.2%
        97.7%
        2.4%
        ERR1442634
        0.4%
        48.0%
        97.2%
        2.6%
        ERR1442635
        0.3%
        47.4%
        97.4%
        1.8%
        ERR1442636
        0.4%
        46.2%
        97.3%
        2.2%
        ERR1442637
        0.5%
        45.2%
        96.7%
        1.5%
        ERR1442638
        0.3%
        46.6%
        97.0%
        1.5%
        ERR1442639
        0.4%
        45.9%
        97.2%
        1.9%
        ERR1442640
        0.4%
        45.4%
        96.9%
        1.8%
        ERR1442641
        0.5%
        46.7%
        97.7%
        5.6%
        ERR1442642
        0.4%
        47.7%
        97.9%
        4.4%
        ERR1442643
        0.3%
        47.4%
        97.4%
        1.9%
        ERR1442644
        0.3%
        47.2%
        97.2%
        1.5%
        ERR1442645
        0.3%
        47.4%
        97.2%
        1.9%
        ERR1442646
        0.5%
        48.3%
        97.3%
        2.2%
        ERR1442647
        0.4%
        47.8%
        97.2%
        1.7%
        ERR1442648
        0.5%
        47.4%
        97.0%
        2.1%
        ERR1442649
        0.6%
        47.1%
        97.5%
        4.3%
        ERR1442650
        0.6%
        46.5%
        97.1%
        4.8%
        ERR1442651
        0.5%
        45.7%
        97.3%
        3.2%
        ERR1442652
        0.7%
        45.3%
        97.2%
        3.0%
        ERR1442653
        0.5%
        46.1%
        97.0%
        1.9%
        ERR1442654
        0.4%
        45.9%
        97.1%
        1.8%
        ERR1442655
        0.4%
        45.6%
        97.0%
        2.1%
        ERR1442691
        0.4%
        47.2%
        97.0%
        1.8%
        ERR1442692
        0.3%
        46.8%
        97.2%
        1.8%
        ERR1442693
        0.4%
        46.9%
        97.2%
        1.7%
        ERR1442694
        0.4%
        46.8%
        97.1%
        1.6%
        ERR1442695
        0.5%
        46.0%
        96.9%
        1.8%
        ERR1442696
        0.4%
        46.7%
        97.3%
        1.7%
        ERR1442697
        0.4%
        46.4%
        97.1%
        1.3%
        ERR1442698
        0.6%
        45.0%
        95.4%
        1.4%
        ERR1442699
        0.4%
        47.1%
        97.0%
        2.1%
        ERR1442700
        0.4%
        46.2%
        96.9%
        1.7%
        ERR1442711
        0.4%
        45.9%
        96.9%
        1.5%
        ERR1442712
        0.4%
        46.7%
        96.9%
        1.8%
        ERR1442713
        0.5%
        45.7%
        96.5%
        1.7%
        ERR1442714
        0.3%
        46.5%
        97.3%
        1.6%
        ERR1442715
        0.4%
        47.3%
        97.5%
        2.4%
        ERR1442716
        0.5%
        47.3%
        97.0%
        2.1%
        ERR1442717
        0.5%
        46.8%
        97.0%
        1.9%
        ERR1442718
        0.5%
        47.2%
        96.9%
        1.9%
        ERR1442719
        0.4%
        47.8%
        97.2%
        1.8%
        ERR1442720
        0.5%
        47.5%
        97.4%
        2.5%
        ERR1442721
        0.3%
        48.7%
        97.4%
        1.6%
        ERR1442722
        0.3%
        47.1%
        96.9%
        1.5%
        ERR1442723
        0.3%
        48.2%
        97.7%
        2.4%
        ERR1442724
        0.4%
        48.0%
        97.2%
        2.6%
        ERR1442725
        0.3%
        47.4%
        97.3%
        1.8%
        ERR1442726
        0.4%
        46.2%
        97.2%
        2.2%
        ERR1442727
        0.5%
        45.2%
        96.6%
        1.5%
        ERR1442728
        0.3%
        46.6%
        96.9%
        1.5%
        ERR1442729
        0.4%
        45.8%
        97.2%
        1.9%
        ERR1442730
        0.4%
        45.4%
        96.9%
        1.8%
        ERR1442731
        0.5%
        46.7%
        97.7%
        5.6%
        ERR1442732
        0.4%
        47.7%
        97.8%
        4.4%
        ERR1442733
        0.3%
        47.4%
        97.3%
        1.8%
        ERR1442734
        0.3%
        47.2%
        97.2%
        1.5%
        ERR1442735
        0.3%
        47.4%
        97.2%
        1.9%
        ERR1442736
        0.5%
        48.2%
        97.3%
        2.2%
        ERR1442737
        0.4%
        47.8%
        97.1%
        1.7%
        ERR1442738
        0.5%
        47.4%
        97.0%
        2.1%
        ERR1442739
        0.6%
        47.1%
        97.4%
        4.2%
        ERR1442740
        0.6%
        46.5%
        97.0%
        4.9%
        ERR1442741
        0.5%
        45.7%
        96.8%
        3.1%
        ERR1442742
        0.7%
        45.3%
        96.7%
        3.0%
        ERR1442743
        0.4%
        46.1%
        96.7%
        1.9%
        ERR1442744
        0.4%
        45.9%
        96.6%
        1.8%
        ERR1442745
        0.4%
        45.7%
        96.5%
        2.1%
        ERR1442781
        0.4%
        47.2%
        96.6%
        1.7%
        ERR1442782
        0.3%
        46.8%
        96.8%
        1.8%
        ERR1442783
        0.4%
        46.9%
        96.8%
        1.7%
        ERR1442784
        0.4%
        46.8%
        96.7%
        1.6%
        ERR1442785
        0.5%
        46.0%
        96.5%
        1.7%
        ERR1442786
        0.4%
        46.8%
        96.8%
        1.7%
        ERR1442787
        0.4%
        46.4%
        96.7%
        1.3%
        ERR1442788
        0.6%
        45.0%
        94.9%
        1.4%
        ERR1442789
        0.4%
        47.1%
        96.6%
        2.1%
        ERR1442790
        0.4%
        46.3%
        96.5%
        1.7%
        ERR1442801
        0.4%
        46.0%
        96.4%
        1.5%
        ERR1442802
        0.4%
        46.7%
        96.5%
        1.8%
        ERR1442803
        0.5%
        45.7%
        96.1%
        1.7%
        ERR1442804
        0.3%
        46.5%
        96.8%
        1.6%
        ERR1442805
        0.4%
        47.3%
        97.1%
        2.4%
        ERR1442806
        0.5%
        47.4%
        96.6%
        2.1%
        ERR1442807
        0.5%
        46.8%
        96.5%
        1.8%
        ERR1442808
        0.5%
        47.2%
        96.5%
        1.9%
        ERR1442809
        0.4%
        47.8%
        96.8%
        1.8%
        ERR1442810
        0.5%
        47.5%
        96.9%
        2.5%
        ERR1442811
        0.3%
        48.7%
        97.0%
        1.6%
        ERR1442812
        0.4%
        47.2%
        96.6%
        1.5%
        ERR1442813
        0.4%
        48.2%
        97.3%
        2.4%
        ERR1442814
        0.4%
        48.0%
        96.8%
        2.6%
        ERR1442815
        0.3%
        47.4%
        96.9%
        1.8%
        ERR1442816
        0.4%
        46.2%
        96.8%
        2.2%
        ERR1442817
        0.6%
        45.2%
        96.3%
        1.5%
        ERR1442818
        0.3%
        46.6%
        96.6%
        1.5%
        ERR1442819
        0.4%
        45.9%
        96.8%
        1.9%
        ERR1442820
        0.4%
        45.4%
        96.4%
        1.8%
        ERR1442821
        0.5%
        46.7%
        97.2%
        5.5%
        ERR1442822
        0.4%
        47.7%
        97.4%
        4.4%
        ERR1442823
        0.3%
        47.4%
        96.9%
        1.8%
        ERR1442824
        0.4%
        47.2%
        96.8%
        1.5%
        ERR1442825
        0.3%
        47.4%
        96.8%
        1.9%
        ERR1442826
        0.5%
        48.3%
        96.8%
        2.2%
        ERR1442827
        0.4%
        47.8%
        96.7%
        1.7%
        ERR1442828
        0.5%
        47.4%
        96.5%
        2.1%
        ERR1442829
        0.6%
        47.1%
        97.0%
        4.2%
        ERR1442830
        0.6%
        46.5%
        96.6%
        4.8%
        ERR1442831
        0.5%
        45.7%
        96.7%
        3.1%
        ERR1442832
        0.6%
        45.3%
        96.6%
        3.0%
        ERR1442833
        0.4%
        46.1%
        96.5%
        1.9%
        ERR1442834
        0.4%
        45.9%
        96.5%
        1.7%
        ERR1442835
        0.4%
        45.7%
        96.3%
        2.1%
        ERR1442871
        0.4%
        47.2%
        96.4%
        1.7%
        ERR1442872
        0.3%
        46.8%
        96.7%
        1.8%
        ERR1442873
        0.4%
        46.9%
        96.6%
        1.7%
        ERR1442874
        0.4%
        46.8%
        96.5%
        1.6%
        ERR1442875
        0.5%
        46.0%
        96.3%
        1.7%
        ERR1442876
        0.3%
        46.8%
        96.7%
        1.7%
        ERR1442877
        0.4%
        46.4%
        96.5%
        1.3%
        ERR1442878
        0.6%
        45.0%
        94.7%
        1.4%
        ERR1442879
        0.4%
        47.1%
        96.4%
        2.0%
        ERR1442880
        0.4%
        46.3%
        96.4%
        1.7%
        ERR1442891
        0.4%
        46.0%
        96.3%
        1.5%
        ERR1442892
        0.4%
        46.7%
        96.3%
        1.8%
        ERR1442893
        0.5%
        45.7%
        95.9%
        1.7%
        ERR1442894
        0.3%
        46.5%
        96.7%
        1.6%
        ERR1442895
        0.4%
        47.3%
        96.9%
        2.4%
        ERR1442896
        0.5%
        47.3%
        96.4%
        2.1%
        ERR1442897
        0.5%
        46.8%
        96.3%
        1.9%
        ERR1442898
        0.5%
        47.2%
        96.3%
        1.8%
        ERR1442899
        0.4%
        47.8%
        96.6%
        1.8%
        ERR1442900
        0.5%
        47.5%
        96.8%
        2.5%
        ERR1442901
        0.3%
        48.7%
        96.9%
        1.6%
        ERR1442902
        0.3%
        47.1%
        96.4%
        1.5%
        ERR1442903
        0.4%
        48.2%
        97.1%
        2.4%
        ERR1442904
        0.4%
        48.0%
        96.5%
        2.6%
        ERR1442905
        0.3%
        47.4%
        96.7%
        1.8%
        ERR1442906
        0.4%
        46.2%
        96.6%
        2.2%
        ERR1442907
        0.5%
        45.2%
        96.0%
        1.5%
        ERR1442908
        0.3%
        46.6%
        96.4%
        1.5%
        ERR1442909
        0.4%
        45.8%
        96.6%
        1.9%
        ERR1442910
        0.4%
        45.4%
        96.3%
        1.8%
        ERR1442911
        0.5%
        46.7%
        97.0%
        5.6%
        ERR1442912
        0.4%
        47.7%
        97.2%
        4.4%
        ERR1442913
        0.3%
        47.4%
        96.7%
        1.8%
        ERR1442914
        0.3%
        47.2%
        96.6%
        1.5%
        ERR1442915
        0.3%
        47.4%
        96.6%
        1.9%
        ERR1442916
        0.5%
        48.3%
        96.7%
        2.2%
        ERR1442917
        0.4%
        47.8%
        96.5%
        1.7%
        ERR1442918
        0.5%
        47.4%
        96.4%
        2.1%
        ERR1442919
        0.6%
        47.1%
        96.8%
        4.2%
        ERR1442920
        0.6%
        46.5%
        96.4%
        4.8%
        Shield-1
        1.9%
        47.2%
        100.0%
        0.0%
        229 bp
        8.3%
        100.0%
        10.5
        0.8 X
        11.6
        0.6
        Shield-2
        1.6%
        46.8%
        100.0%
        0.0%
        229 bp
        7.4%
        100.0%
        11.5
        0.9 X
        12.5
        0.7
        Shield-3
        1.8%
        46.9%
        100.0%
        0.0%
        235 bp
        8.0%
        100.0%
        13.1
        1.1 X
        14.6
        0.7
        Shield-4
        1.8%
        46.8%
        100.0%
        0.0%
        238 bp
        7.4%
        100.0%
        12.2
        1.0 X
        13.5
        0.6
        Shield-5
        2.0%
        46.0%
        100.0%
        0.0%
        230 bp
        7.8%
        100.0%
        11.8
        1.0 X
        13.1
        0.7

        Workflow explanation

        Preprocessing of reads was done automatically with workflow tool seq2science v0.6.1. Public samples were downloaded from the Sequence Read Archive with help of the ncbi e-utilities and pysradb. Genome assembly GRCz11 was downloaded with genomepy 0.11.0. Paired-end reads were trimmed with fastp v0.20.1 with default options. Reads were aligned with STAR v2.7.6a with default options. Transcript abundances were quantified with Salmon v1.5.2 with options '--seqBias --gcBias --validateMappings --recoverOrphans'. Afterwards, duplicate reads were marked with Picard MarkDuplicates v2.23.8. Transcript abundance estimations were aggregated and converted to gene counts using tximeta v1.10.0. Mapped reads were removed if they did not have a minimum mapping quality of 255, were a (secondary) multimapper or aligned inside the ENCODE blacklist.Afterwards samples were downsampled to -1 reads. General alignment statistics were collected by samtools stats v1.14. Sample sequencing strandedness was inferred using RSeQC v4.0.0 in order to improve quantification accuracy. Deeptools v3.5.0 was used for the fingerprint, profile, correlation and dendrogram/heatmap plots, where the heatmap was made with options '--distanceBetweenBins 9000 --binSize 1000'. RNA-seq read duplication types were analyzed using dupRadar v1.20.0. The UCSC genome browser was used to visualize and inspect alignment. Quality control metrics were aggregated by MultiQC v1.11.

        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
        ERR1442646 GRCz11 1-cell 1-cell-1 0hpf_D1
        ERR1442736 GRCz11 1-cell 1-cell-1 0hpf_D2
        ERR1442826 GRCz11 1-cell 1-cell-1 0hpf_D3
        ERR1442916 GRCz11 1-cell 1-cell-1 0hpf_D4
        ERR1442647 GRCz11 1-cell 1-cell-2 0hpf_D5
        ERR1442737 GRCz11 1-cell 1-cell-2 0hpf_D6
        ERR1442827 GRCz11 1-cell 1-cell-2 0hpf_D7
        ERR1442917 GRCz11 1-cell 1-cell-2 0hpf_D8
        ERR1442648 GRCz11 1-cell 1-cell-3 0hpf_D9
        ERR1442738 GRCz11 1-cell 1-cell-3 0hpf_D10
        ERR1442828 GRCz11 1-cell 1-cell-3 0hpf_D11
        ERR1442918 GRCz11 1-cell 1-cell-3 0hpf_D12
        ERR1442649 GRCz11 1-cell 1-cell-4 0hpf_D13
        ERR1442739 GRCz11 1-cell 1-cell-4 0hpf_D14
        ERR1442829 GRCz11 1-cell 1-cell-4 0hpf_D15
        ERR1442919 GRCz11 1-cell 1-cell-4 0hpf_D16
        ERR1442650 GRCz11 1-cell 1-cell-5 0hpf_D17
        ERR1442740 GRCz11 1-cell 1-cell-5 0hpf_D18
        ERR1442830 GRCz11 1-cell 1-cell-5 0hpf_D19
        ERR1442920 GRCz11 1-cell 1-cell-5 0hpf_D20
        ERR1442626 GRCz11 2-cell 2-cell-1 0.75hpf_D21
        ERR1442716 GRCz11 2-cell 2-cell-1 0.75hpf_D22
        ERR1442806 GRCz11 2-cell 2-cell-1 0.75hpf_D23
        ERR1442896 GRCz11 2-cell 2-cell-1 0.75hpf_D24
        ERR1442627 GRCz11 2-cell 2-cell-2 0.75hpf_D25
        ERR1442717 GRCz11 2-cell 2-cell-2 0.75hpf_D26
        ERR1442807 GRCz11 2-cell 2-cell-2 0.75hpf_D27
        ERR1442897 GRCz11 2-cell 2-cell-2 0.75hpf_D28
        ERR1442628 GRCz11 2-cell 2-cell-3 0.75hpf_D29
        ERR1442718 GRCz11 2-cell 2-cell-3 0.75hpf_D30
        ERR1442808 GRCz11 2-cell 2-cell-3 0.75hpf_D31
        ERR1442898 GRCz11 2-cell 2-cell-3 0.75hpf_D32
        ERR1442629 GRCz11 2-cell 2-cell-4 0.75hpf_D33
        ERR1442719 GRCz11 2-cell 2-cell-4 0.75hpf_D34
        ERR1442809 GRCz11 2-cell 2-cell-4 0.75hpf_D35
        ERR1442899 GRCz11 2-cell 2-cell-4 0.75hpf_D36
        ERR1442630 GRCz11 2-cell 2-cell-5 0.75hpf_D37
        ERR1442720 GRCz11 2-cell 2-cell-5 0.75hpf_D38
        ERR1442810 GRCz11 2-cell 2-cell-5 0.75hpf_D39
        ERR1442900 GRCz11 2-cell 2-cell-5 0.75hpf_D40
        ERR1442631 GRCz11 128-cell 128-cell-1 2.25hpf_D41
        ERR1442721 GRCz11 128-cell 128-cell-1 2.25hpf_D42
        ERR1442811 GRCz11 128-cell 128-cell-1 2.25hpf_D43
        ERR1442901 GRCz11 128-cell 128-cell-1 2.25hpf_D44
        ERR1442632 GRCz11 128-cell 128-cell-2 2.25hpf_D45
        ERR1442722 GRCz11 128-cell 128-cell-2 2.25hpf_D46
        ERR1442812 GRCz11 128-cell 128-cell-2 2.25hpf_D47
        ERR1442902 GRCz11 128-cell 128-cell-2 2.25hpf_D48
        ERR1442633 GRCz11 128-cell 128-cell-3 2.25hpf_D49
        ERR1442723 GRCz11 128-cell 128-cell-3 2.25hpf_D50
        ERR1442813 GRCz11 128-cell 128-cell-3 2.25hpf_D51
        ERR1442903 GRCz11 128-cell 128-cell-3 2.25hpf_D52
        ERR1442634 GRCz11 128-cell 128-cell-4 2.25hpf_D53
        ERR1442724 GRCz11 128-cell 128-cell-4 2.25hpf_D54
        ERR1442814 GRCz11 128-cell 128-cell-4 2.25hpf_D55
        ERR1442904 GRCz11 128-cell 128-cell-4 2.25hpf_D56
        ERR1442635 GRCz11 128-cell 128-cell-5 2.25hpf_D57
        ERR1442725 GRCz11 128-cell 128-cell-5 2.25hpf_D58
        ERR1442815 GRCz11 128-cell 128-cell-5 2.25hpf_D59
        ERR1442905 GRCz11 128-cell 128-cell-5 2.25hpf_D60
        ERR1442641 GRCz11 1k-cell 1k-cell-1 3hpf_D61
        ERR1442731 GRCz11 1k-cell 1k-cell-1 3hpf_D62
        ERR1442821 GRCz11 1k-cell 1k-cell-1 3hpf_D63
        ERR1442911 GRCz11 1k-cell 1k-cell-1 3hpf_D64
        ERR1442642 GRCz11 1k-cell 1k-cell-2 3hpf_D65
        ERR1442732 GRCz11 1k-cell 1k-cell-2 3hpf_D66
        ERR1442822 GRCz11 1k-cell 1k-cell-2 3hpf_D67
        ERR1442912 GRCz11 1k-cell 1k-cell-2 3hpf_D68
        ERR1442643 GRCz11 1k-cell 1k-cell-3 3hpf_D69
        ERR1442733 GRCz11 1k-cell 1k-cell-3 3hpf_D70
        ERR1442823 GRCz11 1k-cell 1k-cell-3 3hpf_D71
        ERR1442913 GRCz11 1k-cell 1k-cell-3 3hpf_D72
        ERR1442644 GRCz11 1k-cell 1k-cell-4 3hpf_D73
        ERR1442734 GRCz11 1k-cell 1k-cell-4 3hpf_D74
        ERR1442824 GRCz11 1k-cell 1k-cell-4 3hpf_D75
        ERR1442914 GRCz11 1k-cell 1k-cell-4 3hpf_D76
        ERR1442645 GRCz11 1k-cell 1k-cell-5 3hpf_D77
        ERR1442735 GRCz11 1k-cell 1k-cell-5 3hpf_D78
        ERR1442825 GRCz11 1k-cell 1k-cell-5 3hpf_D79
        ERR1442915 GRCz11 1k-cell 1k-cell-5 3hpf_D80
        ERR1442621 GRCz11 Dome Dome-1 4.33hpf_D81
        ERR1442711 GRCz11 Dome Dome-1 4.33hpf_D82
        ERR1442801 GRCz11 Dome Dome-1 4.33hpf_D83
        ERR1442891 GRCz11 Dome Dome-1 4.33hpf_D84
        ERR1442622 GRCz11 Dome Dome-2 4.33hpf_D85
        ERR1442712 GRCz11 Dome Dome-2 4.33hpf_D86
        ERR1442802 GRCz11 Dome Dome-2 4.33hpf_D87
        ERR1442892 GRCz11 Dome Dome-2 4.33hpf_D88
        ERR1442623 GRCz11 Dome Dome-3 4.33hpf_D89
        ERR1442713 GRCz11 Dome Dome-3 4.33hpf_D90
        ERR1442803 GRCz11 Dome Dome-3 4.33hpf_D91
        ERR1442893 GRCz11 Dome Dome-3 4.33hpf_D92
        ERR1442624 GRCz11 Dome Dome-4 4.33hpf_D93
        ERR1442714 GRCz11 Dome Dome-4 4.33hpf_D94
        ERR1442804 GRCz11 Dome Dome-4 4.33hpf_D95
        ERR1442894 GRCz11 Dome Dome-4 4.33hpf_D96
        ERR1442625 GRCz11 Dome Dome-5 4.33hpf_D97
        ERR1442715 GRCz11 Dome Dome-5 4.33hpf_D98
        ERR1442805 GRCz11 Dome Dome-5 4.33hpf_D99
        ERR1442895 GRCz11 Dome Dome-5 4.33hpf_D100
        ERR1442561 GRCz11 50pc-epiboly 50pc-epiboly-1 5.25hpf_D101
        ERR1442651 GRCz11 50pc-epiboly 50pc-epiboly-1 5.25hpf_D102
        ERR1442741 GRCz11 50pc-epiboly 50pc-epiboly-1 5.25hpf_D103
        ERR1442831 GRCz11 50pc-epiboly 50pc-epiboly-1 5.25hpf_D104
        ERR1442562 GRCz11 50pc-epiboly 50pc-epiboly-2 5.25hpf_D105
        ERR1442652 GRCz11 50pc-epiboly 50pc-epiboly-2 5.25hpf_D106
        ERR1442742 GRCz11 50pc-epiboly 50pc-epiboly-2 5.25hpf_D107
        ERR1442832 GRCz11 50pc-epiboly 50pc-epiboly-2 5.25hpf_D108
        ERR1442563 GRCz11 50pc-epiboly 50pc-epiboly-3 5.25hpf_D109
        ERR1442653 GRCz11 50pc-epiboly 50pc-epiboly-3 5.25hpf_D110
        ERR1442743 GRCz11 50pc-epiboly 50pc-epiboly-3 5.25hpf_D111
        ERR1442833 GRCz11 50pc-epiboly 50pc-epiboly-3 5.25hpf_D112
        ERR1442564 GRCz11 50pc-epiboly 50pc-epiboly-4 5.25hpf_D113
        ERR1442654 GRCz11 50pc-epiboly 50pc-epiboly-4 5.25hpf_D114
        ERR1442744 GRCz11 50pc-epiboly 50pc-epiboly-4 5.25hpf_D115
        ERR1442834 GRCz11 50pc-epiboly 50pc-epiboly-4 5.25hpf_D116
        ERR1442565 GRCz11 50pc-epiboly 50pc-epiboly-5 5.25hpf_D117
        ERR1442655 GRCz11 50pc-epiboly 50pc-epiboly-5 5.25hpf_D118
        ERR1442745 GRCz11 50pc-epiboly 50pc-epiboly-5 5.25hpf_D119
        ERR1442835 GRCz11 50pc-epiboly 50pc-epiboly-5 5.25hpf_D120
        ERR1442601 GRCz11 Shield Shield-1 6hpf_D121
        ERR1442691 GRCz11 Shield Shield-1 6hpf_D122
        ERR1442781 GRCz11 Shield Shield-1 6hpf_D123
        ERR1442871 GRCz11 Shield Shield-1 6hpf_D124
        ERR1442602 GRCz11 Shield Shield-2 6hpf_D125
        ERR1442692 GRCz11 Shield Shield-2 6hpf_D126
        ERR1442782 GRCz11 Shield Shield-2 6hpf_D127
        ERR1442872 GRCz11 Shield Shield-2 6hpf_D128
        ERR1442603 GRCz11 Shield Shield-3 6hpf_D129
        ERR1442693 GRCz11 Shield Shield-3 6hpf_D130
        ERR1442783 GRCz11 Shield Shield-3 6hpf_D131
        ERR1442873 GRCz11 Shield Shield-3 6hpf_D132
        ERR1442604 GRCz11 Shield Shield-4 6hpf_D133
        ERR1442694 GRCz11 Shield Shield-4 6hpf_D134
        ERR1442784 GRCz11 Shield Shield-4 6hpf_D135
        ERR1442874 GRCz11 Shield Shield-4 6hpf_D136
        ERR1442605 GRCz11 Shield Shield-5 6hpf_D137
        ERR1442695 GRCz11 Shield Shield-5 6hpf_D138
        ERR1442785 GRCz11 Shield Shield-5 6hpf_D139
        ERR1442875 GRCz11 Shield Shield-5 6hpf_D140
        ERR1442606 GRCz11 75pc-epiboly 75pc-epiboly-1 8hpf_D141
        ERR1442696 GRCz11 75pc-epiboly 75pc-epiboly-1 8hpf_D142
        ERR1442786 GRCz11 75pc-epiboly 75pc-epiboly-1 8hpf_D143
        ERR1442876 GRCz11 75pc-epiboly 75pc-epiboly-1 8hpf_D144
        ERR1442607 GRCz11 75pc-epiboly 75pc-epiboly-2 8hpf_D145
        ERR1442697 GRCz11 75pc-epiboly 75pc-epiboly-2 8hpf_D146
        ERR1442787 GRCz11 75pc-epiboly 75pc-epiboly-2 8hpf_D147
        ERR1442877 GRCz11 75pc-epiboly 75pc-epiboly-2 8hpf_D148
        ERR1442608 GRCz11 75pc-epiboly 75pc-epiboly-3 8hpf_D149
        ERR1442698 GRCz11 75pc-epiboly 75pc-epiboly-3 8hpf_D150
        ERR1442788 GRCz11 75pc-epiboly 75pc-epiboly-3 8hpf_D151
        ERR1442878 GRCz11 75pc-epiboly 75pc-epiboly-3 8hpf_D152
        ERR1442609 GRCz11 75pc-epiboly 75pc-epiboly-4 8hpf_D153
        ERR1442699 GRCz11 75pc-epiboly 75pc-epiboly-4 8hpf_D154
        ERR1442789 GRCz11 75pc-epiboly 75pc-epiboly-4 8hpf_D155
        ERR1442879 GRCz11 75pc-epiboly 75pc-epiboly-4 8hpf_D156
        ERR1442610 GRCz11 75pc-epiboly 75pc-epiboly-5 8hpf_D157
        ERR1442700 GRCz11 75pc-epiboly 75pc-epiboly-5 8hpf_D158
        ERR1442790 GRCz11 75pc-epiboly 75pc-epiboly-5 8hpf_D159
        ERR1442880 GRCz11 75pc-epiboly 75pc-epiboly-5 8hpf_D160
        ERR1442636 GRCz11 1-4-somites 1-4-somites-1 10.33hpf_D161
        ERR1442726 GRCz11 1-4-somites 1-4-somites-1 10.33hpf_D162
        ERR1442816 GRCz11 1-4-somites 1-4-somites-1 10.33hpf_D163
        ERR1442906 GRCz11 1-4-somites 1-4-somites-1 10.33hpf_D164
        ERR1442637 GRCz11 1-4-somites 1-4-somites-2 10.33hpf_D165
        ERR1442727 GRCz11 1-4-somites 1-4-somites-2 10.33hpf_D166
        ERR1442817 GRCz11 1-4-somites 1-4-somites-2 10.33hpf_D167
        ERR1442907 GRCz11 1-4-somites 1-4-somites-2 10.33hpf_D168
        ERR1442638 GRCz11 1-4-somites 1-4-somites-3 10.33hpf_D169
        ERR1442728 GRCz11 1-4-somites 1-4-somites-3 10.33hpf_D170
        ERR1442818 GRCz11 1-4-somites 1-4-somites-3 10.33hpf_D171
        ERR1442908 GRCz11 1-4-somites 1-4-somites-3 10.33hpf_D172
        ERR1442639 GRCz11 1-4-somites 1-4-somites-4 10.33hpf_D173
        ERR1442729 GRCz11 1-4-somites 1-4-somites-4 10.33hpf_D174
        ERR1442819 GRCz11 1-4-somites 1-4-somites-4 10.33hpf_D175
        ERR1442909 GRCz11 1-4-somites 1-4-somites-4 10.33hpf_D176
        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

        The config file used for this run: 
        # tab-separated file of the samples
samples: samples_pt4.tsv

# pipeline file locations
result_dir: .  # where to store results
genome_dir: ./genomes  # where to look for or download the genomes
fastq_dir: ./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.