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        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.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        About MultiQC

        This report was generated using MultiQC, version 1.11

        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
        atac-seq
        Date
        January 14, 2022
        Project
        atac
        Contact E-mail
        tessa.dewijs2@ru.nl

        Report generated on 2022-01-17, 18:59 based on data in:

        Change sample names:

        General Statistics

        Showing 52/52 rows and 16/33 columns.
        Sample Name% DuplicationGC content% PF% AdapterInsert Size% Dups% MappedM Total seqs% Proper PairsM Total seqs% AssignedGenome coverageM Genome readsM MT genome readsNumber of PeaksTreatment Redundancy
        GSM1859511
        10.6%
        47.1%
        98.2%
        10.3%
        115 bp
        26.3%
        97.7%
        353.2
        98.6%
        111.5
        55.8%
        10.5 X
        298.4
        46.6
        240278
        0.32
        GSM1859512
        4.0%
        51.5%
        99.1%
        12.5%
        109 bp
        13.0%
        47.7%
        137.1
        98.1%
        24.8
        36.6%
        2.0 X
        57.8
        7.6
        101132
        0.12
        GSM2715426
        61.2%
        52.2%
        94.3%
        65.0%
        105 bp
        62.8%
        50.6%
        134.2
        97.7%
        8.4
        4.1%
        4.1 X
        51.9
        16.6
        3769
        0.11
        GSM2715427
        13.9%
        49.8%
        95.9%
        63.0%
        72 bp
        31.1%
        55.3%
        46.7
        99.3%
        8.0
        2.3%
        1.4 X
        18.3
        7.7
        1633
        0.20
        GSM2715428
        37.3%
        48.7%
        95.8%
        70.2%
        73 bp
        49.1%
        63.5%
        65.4
        98.8%
        9.4
        3.2%
        2.2 X
        30.5
        11.5
        1048
        0.13
        GSM2715429
        25.0%
        49.6%
        88.6%
        55.7%
        111 bp
        27.3%
        69.4%
        57.9
        98.6%
        12.1
        3.5%
        2.9 X
        37.5
        3.2
        1770
        0.05
        GSM2715430
        46.2%
        50.9%
        93.1%
        71.0%
        88 bp
        44.0%
        63.0%
        67.8
        98.7%
        11.6
        3.5%
        3.0 X
        39.9
        3.3
        3644
        0.12
        GSM2715431
        19.7%
        48.6%
        96.8%
        73.3%
        74 bp
        22.3%
        59.1%
        73.3
        99.2%
        17.3
        2.3%
        3.0 X
        41.3
        2.5
        2342
        0.14
        GSM2715432
        26.1%
        46.6%
        95.6%
        68.0%
        96 bp
        26.6%
        63.3%
        118.0
        98.8%
        21.2
        2.7%
        5.5 X
        70.7
        4.6
        9698
        0.11
        GSM2715433
        31.2%
        50.1%
        98.3%
        74.4%
        75 bp
        31.6%
        56.3%
        74.2
        99.5%
        14.2
        2.2%
        2.9 X
        38.5
        3.6
        8578
        0.21
        GSM2715434
        12.4%
        47.3%
        97.0%
        67.0%
        78 bp
        17.4%
        58.5%
        88.9
        99.2%
        20.3
        2.1%
        3.6 X
        48.0
        4.5
        6763
        0.21
        GSM2715435
        20.8%
        46.5%
        97.5%
        71.9%
        95 bp
        26.3%
        85.6%
        83.6
        99.5%
        27.4
        4.3%
        4.8 X
        64.4
        7.9
        44760
        0.06
        GSM2715436
        6.2%
        45.8%
        93.9%
        57.3%
        116 bp
        7.6%
        86.5%
        47.8
        99.1%
        16.9
        3.9%
        3.2 X
        40.7
        1.1
        10696
        0.03
        GSM2715437
        19.4%
        46.3%
        91.6%
        48.5%
        145 bp
        22.0%
        89.6%
        76.1
        98.1%
        19.8
        4.9%
        5.8 X
        66.1
        3.0
        27777
        0.04
        GSM2715438
        45.1%
        47.7%
        95.0%
        56.5%
        143 bp
        45.6%
        72.5%
        115.1
        97.8%
        15.0
        8.1%
        6.2 X
        75.9
        8.5
        29277
        0.07
        GSM2715439
        21.3%
        46.4%
        95.4%
        64.7%
        100 bp
        22.6%
        77.7%
        74.2
        99.0%
        20.6
        6.2%
        4.2 X
        55.7
        2.7
        30115
        0.05
        GSM2715440
        26.4%
        47.2%
        96.2%
        55.9%
        132 bp
        27.8%
        80.5%
        58.5
        98.8%
        13.2
        7.8%
        3.7 X
        45.0
        2.8
        26714
        0.05
        GSM2837489
        5.5%
        46.3%
        99.0%
        12.4%
        104 bp
        15.4%
        96.5%
        160.9
        98.7%
        60.9
        53.9%
        5.1 X
        145.5
        9.7
        177322
        0.24
        GSM2837490
        8.3%
        46.0%
        99.0%
        13.2%
        103 bp
        18.9%
        96.4%
        185.5
        98.7%
        67.7
        49.0%
        5.8 X
        165.6
        13.1
        172738
        0.22
        GSM2837491
        4.9%
        47.8%
        99.0%
        12.1%
        141 bp
        14.7%
        83.6%
        146.5
        97.6%
        39.6
        29.0%
        3.8 X
        108.3
        14.0
        148024
        0.12
        GSM2837492
        26.1%
        45.0%
        95.8%
        16.0%
        101 bp
        30.6%
        95.0%
        90.4
        98.2%
        23.4
        29.0%
        2.7 X
        78.0
        7.9
        99948
        0.08
        GSM2837493
        14.3%
        45.0%
        99.3%
        9.8%
        146 bp
        22.4%
        97.3%
        149.9
        97.2%
        41.8
        31.3%
        4.6 X
        129.8
        16.1
        164998
        0.11
        GSM2837494
        19.8%
        44.4%
        99.3%
        9.0%
        150 bp
        32.4%
        96.8%
        167.1
        96.5%
        39.1
        28.2%
        4.7 X
        132.4
        29.4
        141915
        0.09
        GSM2837495
        3.8%
        45.9%
        80.2%
        8.7%
        136 bp
        12.3%
        95.0%
        134.8
        98.0%
        41.0
        27.9%
        4.2 X
        118.9
        9.1
        162625
        0.10
        GSM2837496
        2.6%
        43.9%
        99.4%
        7.2%
        153 bp
        5.8%
        97.7%
        102.8
        97.8%
        34.2
        11.1%
        3.4 X
        96.9
        3.5
        88898
        0.05
        GSM2837497
        5.1%
        45.6%
        89.4%
        9.7%
        123 bp
        19.4%
        96.7%
        136.6
        97.6%
        40.9
        32.0%
        3.9 X
        111.6
        20.5
        160201
        0.12
        GSM2837498
        5.3%
        44.8%
        99.4%
        7.7%
        142 bp
        11.2%
        96.4%
        85.5
        97.7%
        26.9
        14.0%
        2.7 X
        76.0
        6.4
        87581
        0.05
        GSM3494508
        4.4%
        43.2%
        96.3%
        1.2%
        112 bp
        25.4%
        75.1%
        259.6
        71.9%
        64.3
        13.5%
        6.6 X
        184.2
        10.9
        102802
        0.08
        GSM3494509
        1.7%
        42.5%
        96.7%
        1.1%
        107 bp
        18.0%
        75.0%
        208.3
        68.6%
        60.5
        11.2%
        5.2 X
        145.7
        10.5
        82782
        0.06
        GSM3494510
        23.9%
        50.4%
        98.4%
        11.8%
        129 bp
        36.6%
        62.0%
        143.6
        98.1%
        21.3
        28.2%
        2.5 X
        70.5
        18.6
        121727
        0.07
        GSM3494511
        23.2%
        48.0%
        98.3%
        15.1%
        118 bp
        31.5%
        81.4%
        173.5
        98.4%
        38.5
        29.4%
        4.3 X
        124.1
        17.1
        140388
        0.11
        GSM3756599
        8.2%
        44.0%
        87.9%
        7.2%
        210 bp
        29.8%
        97.1%
        51.7
        93.8%
        6.7
        2.7%
        1.9 X
        35.5
        14.9
        4064
        0.02
        GSM3756600
        23.7%
        45.0%
        97.7%
        7.1%
        190 bp
        48.3%
        89.4%
        150.8
        95.9%
        15.8
        2.5%
        5.3 X
        98.6
        36.5
        23530
        0.03
        GSM3756601
        6.8%
        46.0%
        99.6%
        34.9%
        89 bp
        16.4%
        95.6%
        132.7
        98.8%
        51.3
        32.7%
        5.7 X
        114.8
        12.4
        110954
        0.16
        GSM3756602
        6.3%
        45.4%
        99.6%
        37.1%
        95 bp
        12.8%
        96.6%
        159.8
        98.6%
        61.5
        28.0%
        7.2 X
        145.2
        9.5
        125750
        0.14
        GSM3756603
        3.3%
        44.4%
        98.5%
        7.2%
        227 bp
        7.9%
        98.6%
        53.0
        92.1%
        7.3
        23.5%
        2.6 X
        48.7
        3.7
        48132
        0.06
        GSM3756604
        7.0%
        43.5%
        100.0%
        8.8%
        200 bp
        20.6%
        93.0%
        111.3
        95.5%
        18.3
        12.2%
        4.6 X
        85.9
        17.9
        48108
        0.05
        GSM3756605
        6.9%
        45.8%
        96.3%
        35.5%
        128 bp
        16.0%
        96.5%
        64.9
        98.8%
        21.5
        10.1%
        3.8 X
        56.6
        6.8
        49843
        0.04
        GSM3756606
        19.1%
        47.3%
        99.6%
        7.0%
        170 bp
        40.4%
        69.3%
        62.4
        94.7%
        6.3
        5.8%
        1.6 X
        29.3
        14.0
        12040
        0.03
        GSM3756607
        11.3%
        46.6%
        99.8%
        10.8%
        178 bp
        25.7%
        88.3%
        77.4
        96.7%
        13.0
        5.7%
        3.0 X
        55.9
        12.7
        41264
        0.04
        GSM3756608
        10.4%
        43.5%
        94.6%
        5.3%
        206 bp
        28.6%
        96.8%
        104.9
        95.5%
        15.1
        3.5%
        4.2 X
        76.8
        25.0
        12604
        0.02
        GSM3756609
        9.2%
        43.5%
        93.9%
        6.9%
        276 bp
        16.1%
        95.7%
        38.7
        89.8%
        4.4
        6.8%
        1.7 X
        32.2
        4.9
        14454
        0.02
        GSM3756610
        3.7%
        44.7%
        97.4%
        9.3%
        183 bp
        27.3%
        81.4%
        80.4
        96.7%
        12.0
        3.3%
        2.6 X
        47.7
        17.9
        8800
        0.04
        GSM3756611
        16.7%
        44.5%
        99.9%
        7.2%
        188 bp
        35.5%
        96.0%
        77.9
        96.3%
        11.2
        5.3%
        2.9 X
        54.1
        20.9
        24095
        0.03
        GSM3756612
        6.7%
        44.3%
        99.5%
        27.7%
        129 bp
        17.7%
        95.8%
        136.8
        98.0%
        41.5
        19.6%
        5.7 X
        112.6
        18.8
        126275
        0.08
        GSM3756613
        6.5%
        45.4%
        99.5%
        34.3%
        112 bp
        12.4%
        95.6%
        138.5
        98.3%
        47.5
        30.2%
        6.2 X
        124.7
        8.0
        121827
        0.15
        GSM3756614
        10.0%
        44.3%
        98.8%
        5.7%
        191 bp
        34.9%
        97.2%
        111.7
        96.3%
        15.4
        11.8%
        4.1 X
        75.2
        33.5
        41209
        0.05
        GSM3756615
        11.8%
        43.4%
        97.0%
        7.1%
        192 bp
        22.1%
        97.1%
        100.4
        96.4%
        18.6
        7.1%
        4.5 X
        82.9
        14.9
        25456
        0.03
        GSM4724541
        9.8%
        48.2%
        97.2%
        28.3%
        58 bp
        16.0%
        88.6%
        184.8
        98.9%
        77.2
        33.4%
        5.3 X
        156.5
        7.2
        192159
        0.14
        GSM4724542
        10.6%
        48.7%
        97.3%
        26.2%
        63 bp
        16.7%
        86.9%
        168.6
        98.9%
        65.8
        37.2%
        4.8 X
        139.4
        7.0
        172617
        0.15
        GSM4724549
        5.5%
        46.3%
        99.0%
        12.4%
        104 bp
        15.4%
        96.5%
        160.9
        98.7%
        60.9
        53.9%
        5.1 X
        145.5
        9.7
        177321
        0.24
        GSM4724550
        8.3%
        46.0%
        99.0%
        13.2%
        103 bp
        18.9%
        96.4%
        185.5
        98.7%
        67.7
        49.0%
        5.8 X
        165.6
        13.1
        172739
        0.22

        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.

        loading..

        Duplication Rates

        Duplication rates of sampled reads.

        loading..

        Insert Sizes

        Insert size estimation of sampled reads.

        loading..

        Sequence Quality

        Average sequencing quality over each base of all reads.

        loading..

        GC Content

        Average GC content over each base of all reads.

        loading..

        N content

        Average N content over each base of all reads.

        loading..

        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..

        SamTools post-sieve

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

        The post-sieve statistics are quality metrics measured after applying (optional) minimum mapping quality, blacklist removal, mitochondrial read removal, 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..

        Read Distribution Profile after Annotation

        Accumulated view of the distribution of sequence reads related to the closest annotated gene. All annotated genes have been normalized to the same size.

        • Green: -2.0Kb upstream of gene to TSS
        • Yellow: TSS to TES
        • Pink: TES to 0.5Kb downstream of gene
        loading..

        macs2_frips

        Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

        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.

        Peak distributions (macs2)

        The distribution of read pileup around 20000 random peaks for each sample. This visualization is a quick and dirty way to check if your peaks look like what you would expect, and what the underlying distribution of different types of peaks is.

        Peak feature distribution (macs2)

        Figure generated by chipseeker

        Distribution of peak locations relative to TSS (macs2)

        Figure generated by chipseeker

        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 biological_replicates descriptive_name
        GSM3756599 GRCz11 256cell 2.5hpf_DA1
        GSM3756600 GRCz11 256cell 2.5hpf_DA2
        GSM3756606 GRCz11 high 3.3hpf_DA3
        GSM3756607 GRCz11 high 3.3hpf_DA4
        GSM3756608 GRCz11 high 3.3hpf_DA5
        GSM3756609 GRCz11 oblong 3.6hpf_DA6
        GSM3756610 GRCz11 oblong 3.6hpf_DA7
        GSM3756611 GRCz11 oblong 3.6hpf_DA8
        GSM3756614 GRCz11 sphere 4hpf_DA9
        GSM3756615 GRCz11 sphere 4hpf_DA10
        GSM2837495 GRCz11 dome 4.3hpf_DB1
        GSM2837497 GRCz11 dome 4.3hpf_DB2
        GSM3756603 GRCz11 dome_2 4.3hpf_DA11
        GSM3756604 GRCz11 dome_2 4.3hpf_DA12
        GSM3756605 GRCz11 dome_2 4.3hpf_DA13
        GSM2837496 GRCz11 shield 6hpf_DB3
        GSM2837498 GRCz11 shield 6hpf_DB4
        GSM3756612 GRCz11 shield_2 6hpf_DA14
        GSM3756613 GRCz11 shield_2 6hpf_DA15
        GSM2837491 GRCz11 80epiboly 8.5hpf_DB5
        GSM2837492 GRCz11 80epiboly 8.5hpf_DB6
        GSM3756601 GRCz11 80epiboly_2 8.5hpf_DA16
        GSM3756602 GRCz11 80epiboly_2 8.5hpf_DA17
        GSM2837493 GRCz11 8somites 13hpf_DB5
        GSM2837494 GRCz11 8somites 13hpf_DB6
        GSM3494511 GRCz11 8somites_2 13hpf_DC1
        GSM3494510 GRCz11 8somites_2 13hpf_DC2
        GSM1859511 GRCz11 24hpf 24hpf_DD1
        GSM1859512 GRCz11 24hpf 24hpf_DD2
        GSM3494509 GRCz11 36hpf 36hpf_DC3
        GSM3494508 GRCz11 36hpf 36hpf_DC4
        GSM2837489 GRCz11 48hpf 48hpf_DB7
        GSM2837490 GRCz11 48hpf 48hpf_DB8
        GSM4724541 GRCz11 24hpf_2 24hpf_DF1
        GSM4724542 GRCz11 24hpf_2 24hpf_DF2
        GSM4724549 GRCz11 48hpf_2 48hpf_DF3
        GSM4724550 GRCz11 48hpf_2 48hpf_DF4
        GSM2715426 GRCz11 64-cell 2hpf_DG1
        GSM2715427 GRCz11 64-cell 2hpf_DG2
        GSM2715428 GRCz11 64-cell 2hpf_DG3
        GSM2715429 GRCz11 256-cell 2.5hpf_DG4
        GSM2715430 GRCz11 256-cell 2.5hpf_DG5
        GSM2715431 GRCz11 256-cell 2.5hpf_DG6
        GSM2715432 GRCz11 1k-cell 3hpf_DG7
        GSM2715433 GRCz11 1k-cell 3hpf_DG8
        GSM2715434 GRCz11 1k-cell 3hpf_DG9
        GSM2715435 GRCz11 oblong_2 3.6hpf_DG10
        GSM2715436 GRCz11 oblong_2 3.6hpf_DG11
        GSM2715437 GRCz11 oblong_2 3.6hpf_DG12
        GSM2715438 GRCz11 dome_3 4.3hpf_DG13
        GSM2715439 GRCz11 dome_3 4.3hpf_DG14
        GSM2715440 GRCz11 dome_3 4.3hpf_DG15

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

# pipeline file locations
result_dir: /bank/tdewijs/atac/atacresults_dre  # where to store results
genome_dir: /bank/tdewijs/genomes  # where to look for or download the genomes
# fastq_dir: ./results/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
biological_replicates: fisher  # change to "keep" to not combine them
technical_replicates: merge    # change to "keep" to not combine them

# which trimmer to use
trimmer: fastp

# which aligner to use
aligner: bwa-mem2

# filtering after alignment
remove_blacklist: true
remove_mito: true
tn5_shift: true
min_mapping_quality: 30
only_primary_align: True
max_template_length: 150
remove_dups: true

# peak callers (supported peak callers are macs2, and genrich)
peak_caller:
  macs2:
      --shift -100 --extsize 200 --nomodel --buffer-size 10000
#  genrich:
#      -j -y -D -d 200 -q 0.05

# how much peak summits will be extended by (on each side) for the final count table
# (e.g. 100 means a 200 bp wide peak)
slop: 100

## differential accessibility analysis
#contrasts:
#  - 'biological_replicates_adult_embryo'

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

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