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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_danRer11_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 v0.9.6, 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
        November 28, 2022
        Project
        seq2science_docs
        Contact E-mail
        yourmail@here.com

        Report generated on 2022-11-28, 14:11 based on data in:

        Change sample names:

        Welcome! Not sure where to start?   Watch a tutorial video   (6:06)

        General Statistics

        Showing 17/17 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
        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
        23515
        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
        110948
        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
        125754
        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
        48109
        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
        49846
        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
        12039
        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
        41265
        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
        12609
        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
        14450
        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
        8803
        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
        126265
        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
        121833
        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
        41215
        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
        25457
        0.03

        Workflow explanation

        Preprocessing of reads was done automatically by seq2science v0.9.6 using the atac-seq workflow. Genome assembly danRer11 was downloaded with genomepy 0.13.0. The effective genome size was estimated per sample by khmer v2.0 by calculating the number of unique kmers with k being the average read length. Paired-end reads were trimmed with fastp v0.20.1 with default options. Reads were aligned with bwa-mem2 v2.2.1 with options '-M'. Afterwards, duplicate reads were marked with Picard MarkDuplicates v2.23.8. General alignment statistics were collected by samtools stats v1.14. Peaks were called with macs2 v2.2.7 with options '--shift -100 --extsize 200 --nomodel --buffer-size 10000' in BAM mode. The effective genome size was estimated by taking the number of unique kmers in the assembly of the same length as the average read length for each sample. Deeptools v3.5.1 was used for the fingerprint, profile, correlation and dendrogram/heatmap plots, where the heatmap was made with options '--distanceBetweenBins 9000 --binSize 1000'. Narrowpeak files of biological replicates belonging to the same condition were merged with fisher's method in macs2. The fraction reads in peak score (frips) was calculated by featurecounts v1.6.4. The UCSC genome browser was used to visualize and inspect alignment. A peak feature distribution plot and peak localization plot relative to TSS were made with chipseeker. A consensus set of summits was made with gimmemotifs.combine_peaks v0.17.1. All summits were extended with 100 bp to get a consensus peakset. Finally, a count table from the consensus peakset was made with gimmemotifs.coverage_table. Differential accessibility analysis was performed using DESeq2 v1.34. To adjust for multiple testing the (default) Benjamini-Hochberg procedure was performed with an FDR cutoff of 0.1 (default is 0.1). Counts were log transformed using the (default) shrinkage estimator apeglm v1.16. Differential peaks analysis on the consensus peakset was performed with gimme maelstrom. Quality control metrics were aggregated by MultiQC v1.11.

        Assembly stats

        Genome assembly danRer11 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 29810 genes.

        fastp

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

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with Highcharts 5.0.6# ReadsChart context menuExport PlotFastp: Filtered ReadsPassed FilterLow QualityToo Many NToo shortGSM3756599GSM3756600GSM3756601GSM3756602GSM3756603GSM3756604GSM3756605GSM3756606GSM3756607GSM3756608GSM3756609GSM3756610GSM3756611GSM3756612GSM3756613GSM3756614GSM375661505M10M15M20M25M30M35M40M45M50M55M60M65M70M75M80M85M90M95M100M105M110M115M120M125M130M135M140M145M150M155M160M165M17…170MCreated with MultiQC

        Duplication Rates

        Duplication rates of sampled reads.

        Created with Highcharts 5.0.6Duplication levelRead percentChart context menuExport PlotFastp: Duplication Rate246810121416182022242628300%20%40%60%80%100%Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with Highcharts 5.0.6Insert sizeRead percentChart context menuExport PlotFastp: Insert Size Distribution01020304050607080901001101201301401501601701801902002102202302402502602700%0.5%1%1.5%2%2.5%3%Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with Highcharts 5.0.6Read PositionR1 Before filtering: Sequence QualityChart context menuExport PlotFastp: Sequence Quality0102030405060708090100110120130140150051015202530354045Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with Highcharts 5.0.6Read PositionR1 Before filtering: Base Content PercentChart context menuExport PlotFastp: Read GC Content01020304050607080901001101201301401500%20%40%60%80%100%Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with Highcharts 5.0.6Read PositionR1 Before filtering: Base Content PercentChart context menuExport PlotFastp: Read N Content01020304050607080901001101201301401500%1%2%3%4%5%6%Created with MultiQC

        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.

        Created with Highcharts 5.0.6Insert Size (bp)CountChart context menuExport PlotPicard: Insert Size0100200300400500600700800900100011001200130014001500160017000100000200000300000400000500000600000Created with MultiQC

        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
        Created with Highcharts 5.0.6# ReadsChart context menuExport PlotPicard: Deduplication StatsUnique PairsUnique UnpairedDuplicate Pairs NonopticalDuplicate UnpairedUnmappedGSM3756599GSM3756600GSM3756601GSM3756602GSM3756603GSM3756604GSM3756605GSM3756606GSM3756607GSM3756608GSM3756609GSM3756610GSM3756611GSM3756612GSM3756613GSM3756614GSM375661502.557.51012.51517.52022.52527.53032.53537.54042.54547.55052.55557.56062.56567.57072.57577.58082.58587.59092.59597.5100Created with MultiQC

        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).

        Created with Highcharts 5.0.6# ReadsChart context menuExport PlotSamtools stats: Alignment ScoresMappedUnmappedGSM3756599GSM3756600GSM3756601GSM3756602GSM3756603GSM3756604GSM3756605GSM3756606GSM3756607GSM3756608GSM3756609GSM3756610GSM3756611GSM3756612GSM3756613GSM3756614GSM375661505M10M15M20M25M30M35M40M45M50M55M60M65M70M75M80M85M90M95M100M105M110M115M120M125M130M135M140M145M150M155M160M165M17…170MCreated with MultiQC

        Alignment metrics

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

        Hover over a data point for more information
        Created with Highcharts 5.0.6020406080100120140Total sequences
        Created with Highcharts 5.0.6020406080100120140Mapped & paired
        Created with Highcharts 5.0.6020406080100120140Properly paired
        Created with Highcharts 5.0.6020406080100120140Duplicated
        Created with Highcharts 5.0.6020406080100120140QC Failed
        Created with Highcharts 5.0.6020406080100120140Reads MQ0
        Created with Highcharts 5.0.601k2k3k4k5k6k7k8k9k10kMapped bases (CIGAR)
        Created with Highcharts 5.0.601k2k3k4k5k6k7k8k9k10kBases Trimmed
        Created with Highcharts 5.0.601k2k3k4k5k6k7k8k9k10kDuplicated bases
        Created with Highcharts 5.0.6020406080100120140Diff chromosomes
        Created with Highcharts 5.0.6020406080100120140Other orientation
        Created with Highcharts 5.0.6020406080100120140Inward pairs
        Created with Highcharts 5.0.6020406080100120140Outward pairs

        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).

        Created with Highcharts 5.0.6# ReadsChart context menuExport PlotSamtools stats: Alignment ScoresMappedGSM3756599GSM3756600GSM3756601GSM3756602GSM3756603GSM3756604GSM3756605GSM3756606GSM3756607GSM3756608GSM3756609GSM3756610GSM3756611GSM3756612GSM3756613GSM3756614GSM375661502.5M5M7.5M10M12.5M15M17.5M20M22.5M25M27.5M30M32.5M35M37.5M40M42.5M45M47.5M50M52.5M55M57.5M60M62.5M65MCreated with MultiQC

        Alignment metrics

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

        Hover over a data point for more information
        Created with Highcharts 5.0.6051015202530354045505560Total sequences
        Created with Highcharts 5.0.6051015202530354045505560Mapped & paired
        Created with Highcharts 5.0.6051015202530354045505560Properly paired
        Created with Highcharts 5.0.6051015202530354045505560Duplicated
        Created with Highcharts 5.0.6051015202530354045505560QC Failed
        Created with Highcharts 5.0.6051015202530354045505560Reads MQ0
        Created with Highcharts 5.0.60500100015002000250030003500Mapped bases (CIGAR)
        Created with Highcharts 5.0.60500100015002000250030003500Bases Trimmed
        Created with Highcharts 5.0.60500100015002000250030003500Duplicated bases
        Created with Highcharts 5.0.6051015202530354045505560Diff chromosomes
        Created with Highcharts 5.0.6051015202530354045505560Other orientation
        Created with Highcharts 5.0.6051015202530354045505560Inward pairs
        Created with Highcharts 5.0.6051015202530354045505560Outward pairs

        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

        Created with Highcharts 5.0.6PC1PC2Chart context menuExport Plotdeeptools: PCA Plot0.19750.20.20250.2050.20750.210.21250.2150.21750.220.22250.2250.22750.230.23250.2350.23750.240.24250.2450.24750.250.25250.2550.2575-0.6-0.5-0.4-0.3-0.2-0.100.10.20.3Created with MultiQC

        Fingerprint plot

        Signal fingerprint according to plotFingerprint

        Created with Highcharts 5.0.6rankFraction w.r.t. bin with highest coverageChart context menuExport PlotdeepTools: Fingerprint plot00.050.10.150.20.250.30.350.40.450.50.550.60.650.70.750.80.850.90.95100.20.40.60.81Created with MultiQC

        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
        Created with Highcharts 5.0.6OccurrenceChart context menuExport Plotdeeptools: Read Distribution Profile after Annotation-2000-1800-1600-1400-1200-1000-800-600-400-20002004006008001000120014000510152025303540Created with MultiQC

        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.

        Created with Highcharts 5.0.6# ReadsChart context menuExport PlotfeatureCounts: AssignmentsAssignedUnassigned: No FeaturesUnassigned: AmbiguityGSM3756599GSM3756600GSM3756601GSM3756602GSM3756603GSM3756604GSM3756605GSM3756606GSM3756607GSM3756608GSM3756609GSM3756610GSM3756611GSM3756612GSM3756613GSM3756614GSM375661501M2M3M4M5M6M7M8M9M10M11M12M13M14M15M16M17M18M19M20M21M22M23M24M25M26M27M28M29M30M31M32M33MCreated with MultiQC

        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.

        Peaks per sample distribution (macs2)

        The distribution of peaks between samples. An upset plot is like a venn diagram, but is easier to read with many samples. This figure shows the overlap of peaks between conditions/samples.

        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.

        biological replicates 80epiboly 256cell combined ma volcano

        biological replicates 80epiboly 256cell pca plot

        gimme maelstrom macs2 results

        Gimme maelstrom is a method to infer differential motifs between samples. It solves a system of linear equations, Ax=b. Where we solve for x, A the motif scores and b the count table. It combines the results of different methods that solve this problem, and its result is the table below. It can be used to find **differential** motifs between samples.

        factors
        (direct or predicted)
        		 motif information z-score
        256cell        		 z-score
        high        		 z-score
        oblong        		 z-score
        sphere        		 z-score
        dome        		 z-score
        shield        		 z-score
        80epiboly        		 %
        with
        motif        		 corr
        256cell        		 corr
        high        		 corr
        oblong        		 corr
        sphere        		 corr
        dome        		 corr
        shield        		 corr
        80epiboly
        GM.5.0.Mixed.0044
        ZGC_162472,HSF1,BRF1A,BRF1B,BRF2, (...)
        		0.25 3.86 4.04 3.90 0.63 -4.87 -4.73
        <1
        		 0.00 0.05 0.05 0.03 0.00 -0.06 -0.04
        GM.5.0.Unknown.0206
        GTF3C2,POLR3G,POLR3A
        		-0.97 0.51 4.13 4.42 3.22 -3.63 -4.56
        <1
        		 -0.02 0.00 0.05 0.06 0.03 -0.03 -0.04
        GM.5.0.C2H2_ZF.0095
        LOC110439851
        		1.73 2.20 1.55 1.14 0.17 -3.02 -2.11
        <1
        		 0.02 0.01 0.02 0.01 0.00 -0.06 -0.01
        GM.5.0.SMAD.0013
        SMAD9,SMAD1,SMAD5
        		0.05 0.12 3.39 0.80 0.63 0.96 -2.64
        <1
        		 -0.05 -0.03 0.06 0.03 0.03 0.02 -0.03
        GM.5.0.Unknown.0128
        GTF3C2,POLR3G,HSF1,HSF4,POLR3A
        		-0.03 2.35 4.24 2.80 -2.33 -3.66 -1.69
        <1
        		 -0.02 0.01 0.04 0.02 0.00 -0.03 -0.01
        GM.5.0.Mixed.0100
        LOC100537384,POU2F2A
        		1.70 2.36 3.05 2.41 0.90 -2.96 -2.73
        <1
        		 0.01 0.01 0.01 0.02 0.01 -0.01 -0.03
        GM.5.0.Unknown.0121
        NO ORTHOLOGS FOUND
        		-0.94 -2.26 -1.30 0.21 -0.57 3.28 1.55
        8
        		 -0.02 -0.04 -0.01 -0.00 0.01 0.03 0.03
        GM.5.0.C2H2_ZF.0281
        NO ORTHOLOGS FOUND
        		0.25 0.91 1.07 0.93 -1.52 -3.35 -0.47
        <1
        		 0.00 0.00 0.01 0.02 0.00 -0.02 -0.01
        GM.5.0.GATA.0018
        GATA3,GATA1B,GATA2A,GATA1A
        		0.71 1.61 3.31 2.09 1.04 -1.87 -1.86
        1
        		 0.02 0.01 0.02 0.01 0.01 -0.04 -0.02
        GM.5.0.bHLH.0086
        OLIG2,OLIG3,BHLHE23,OLIG1
        		1.04 3.03 0.81 0.58 -0.12 -1.19 -1.98
        1
        		 -0.01 0.01 0.01 0.01 0.00 -0.00 -0.01
        GM.5.0.C2H2_ZF.0179
        HIC1
        		3.76 2.71 3.22 0.04 -3.21 -3.46 -0.48
        <1
        		 0.02 0.01 0.01 -0.01 -0.00 -0.02 -0.01
        GM.5.0.C2H2_ZF.0249
        LOC101883970,TCF12,TCF4,PRDM5,LOC110439851, (...)
        		2.78 1.10 -1.84 -3.02 -2.96 -2.06 2.32
        1
        		 0.01 0.00 -0.04 -0.07 -0.06 0.00 0.09
        GM.5.0.E2F.0013
        E2F7,E2F8,E2F1
        		-2.59 -3.65 -0.85 0.26 0.69 1.74 2.13
        <1
        		 -0.07 -0.08 0.01 0.03 0.02 0.04 0.06
        GM.5.0.Nuclear_receptor.0082
        HNF4A,ESRRA,PPARGC1A,ESRRGA,ESRRGB, (...)
        		1.55 3.79 0.77 -0.31 -0.19 -1.04 -2.21
        1
        		 0.02 0.03 -0.03 -0.04 -0.02 -0.02 0.02
        GM.5.0.p53.0011
        TP63,TP73,TP53,NO ORTHOLOGS FOUND,MDM2, (...)
        		3.67 1.22 -1.84 0.36 -0.17 -1.79 -0.89
        <1
        		 0.04 0.01 -0.03 -0.02 -0.01 -0.01 -0.01
        GM.5.0.bZIP.0031
        DDIT3,CEBPA
        		-2.99 -0.80 0.33 2.08 3.36 0.97 -0.80
        1
        		 -0.04 -0.03 0.01 0.02 0.04 0.02 0.01
        GM.5.0.bHLH.0087
        SI_CH211-246M6.4,TCF15,SCXA,SCXB
        		3.77 2.99 0.44 -1.21 0.03 -1.60 -1.94
        <1
        		 0.03 0.01 -0.03 -0.03 -0.01 0.01 -0.00
        GM.5.0.Nuclear_receptor.0149
        PGR,AR,NR3C1
        		-0.94 -1.79 2.45 3.44 3.15 0.59 -1.56
        1
        		 -0.02 -0.03 0.00 0.03 0.04 0.01 -0.01
        GM.5.0.C2H2_ZF.0171
        NO ORTHOLOGS FOUND
        		1.51 1.41 1.12 1.63 0.15 -3.08 -1.09
        1
        		 0.01 0.02 0.02 0.03 0.02 -0.04 -0.04
        GM.5.0.C2H2_ZF.0038
        PRDM14,ZEB2A,ZEB2B,ZEB1B
        		0.43 -0.94 -0.56 1.69 3.06 0.41 -1.76
        1
        		 0.01 -0.00 -0.01 0.01 0.04 -0.02 -0.02
        GM.5.0.bZIP.0054
        MAFAA,MAFBA,MAFA,MAFB,MAFK, (...)
        		0.85 1.64 -1.43 -3.57 -2.21 1.91 1.54
        <1
        		 0.02 -0.00 -0.03 -0.05 0.01 0.03 -0.00
        GM.5.0.THAP_finger.0002
        HIC1,HIC2,SI_DKEY-34M19.3,THAP1,ZGC_122991, (...)
        		1.36 1.61 1.33 0.95 -2.18 -4.28 -1.28
        <1
        		 -0.02 -0.01 0.01 0.01 0.01 -0.03 0.02
        GM.5.0.C2H2_ZF.0094
        NO ORTHOLOGS FOUND
        		2.93 1.87 1.30 1.92 1.79 -1.83 -3.77
        1
        		 0.02 -0.00 -0.02 0.01 0.04 0.03 -0.05
        GM.5.0.C2H2_ZF.0123
        NO ORTHOLOGS FOUND
        		-0.64 -0.03 0.56 3.19 1.90 0.28 -1.62
        <1
        		 -0.01 -0.01 0.00 0.01 0.04 0.01 -0.02
        GM.5.0.C2H2_ZF.0252
        NO ORTHOLOGS FOUND
        		0.59 0.54 3.15 -0.27 -0.05 -0.57 -1.30
        1
        		 -0.01 -0.01 0.00 -0.01 0.01 0.01 0.01
        GM.5.0.SAND.0007
        AIRE
        		2.01 2.68 0.88 -0.06 -1.79 -3.22 -1.17
        <1
        		 0.00 0.00 0.01 0.00 -0.01 -0.03 0.02
        GM.5.0.E2F.0005
        E2F3,SI_CH211-160F23.5,E2F1,E2F4,E2F5
        		-0.67 0.21 1.77 2.87 2.23 0.67 -3.26
        <1
        		 -0.06 -0.06 0.04 0.06 0.06 0.01 -0.01
        GM.5.0.Homeodomain.0179
        TLX1,TLX3B,LOC100008066,TLX2
        		2.50 2.06 0.58 -2.62 -3.82 -1.09 0.77
        1
        		 0.03 0.01 0.01 -0.03 -0.01 -0.02 0.00
        GM.5.0.Mixed.0017
        GTF3C2,POLR3G,POLR3A
        		0.08 0.79 0.08 -2.15 -3.18 0.13 0.90
        <1
        		 -0.03 -0.02 -0.02 -0.03 -0.02 0.01 0.07
        GM.5.0.Mixed.0063
        NFKB1,BCL3
        		3.18 2.30 0.73 -0.76 -1.54 -2.32 -0.41
        1
        		 0.03 0.03 0.00 -0.01 -0.01 -0.03 -0.01
        GM.5.0.Mixed.0104
        ZGC_162472,BRF1A,BRF1B,BRF2,LOC100536580, (...)
        		0.38 1.48 2.32 1.45 0.39 -1.36 -3.23
        <1
        		 0.01 0.02 0.01 0.01 0.03 0.00 -0.05
        GM.5.0.T-box.0019
        EOMESB,TBR1A,TBX5A,TBX21,TBX5B, (...)
        		1.38 0.15 0.34 -3.16 -0.04 3.02 -1.75
        2
        		 0.02 -0.01 -0.00 -0.03 0.01 0.03 -0.02
        GM.5.0.Mixed.0109
        SI_CH211-154O6.2,ZNF384L,NO ORTHOLOGS FOUND,MEF2CB,FOXP3A, (...)
        		-1.83 -2.26 0.40 0.41 -0.86 0.07 3.35
        <1
        		 -0.07 -0.09 -0.03 -0.02 -0.02 0.03 0.15
        GM.5.0.bZIP.0070
        MAFGB,MAFK,MAFF
        		1.71 2.99 0.03 -3.64 -2.95 -3.62 0.39
        1
        		 0.02 0.03 -0.03 -0.06 -0.05 -0.00 0.05
        GM.5.0.C2H2_ZF_Homeodomain.0003
        NO ORTHOLOGS FOUND,ZEB2A,PAX2B,ZEB1B,PAX2A, (...)
        		-0.81 -3.83 -2.20 -1.09 -1.17 2.27 1.86
        <1
        		 -0.05 -0.08 -0.03 -0.00 0.00 0.05 0.08
        GM.5.0.STAT.0002
        NO ORTHOLOGS FOUND,NFATC4,NFATC3A,NFATC1,NFATC2A, (...)
        		-3.02 -0.82 1.77 2.55 1.05 -0.00 1.31
        1
        		 -0.06 -0.06 0.01 0.03 0.03 0.03 0.05
        GM.5.0.C2H2_ZF.0058
        ZIC5,ZIC4,ZIC1,LOC110438163,ZIC6, (...)
        		1.02 1.37 0.44 -0.98 -3.71 -1.97 2.21
        <1
        		 -0.03 -0.01 -0.01 -0.00 -0.01 0.01 0.03
        GM.5.0.Ets.0021
        NO ORTHOLOGS FOUND,FEV,EF1,NR2C2,ETS2, (...)
        		-2.87 -2.41 1.99 1.39 2.24 3.01 -1.39
        <1
        		 -0.06 -0.07 0.03 0.05 0.06 0.04 -0.01
        GM.5.0.C2H2_ZF.0224
        YY1A,MBTPS2,YY1B
        		0.14 1.97 2.45 3.07 0.93 -2.74 -2.85
        <1
        		 -0.01 0.01 0.03 0.03 0.03 -0.03 -0.04
        GM.5.0.bHLH.0071
        LOC101883970,TCF4,TCF3B,TCF12,MYF5, (...)
        		2.93 3.32 -1.10 -1.21 -3.14 -2.30 1.53
        1
        		 0.04 0.01 -0.03 -0.05 -0.02 0.01 0.01
        GM.5.0.C2H2_ZF.0040
        REST,BCL3,SIN3B,SIN3AB,SIN3AA
        		3.03 3.18 3.29 0.72 -0.39 -3.53 -2.21
        1
        		 0.03 0.03 0.02 0.00 0.00 -0.03 -0.04
        GM.5.0.Homeodomain.0148
        NO ORTHOLOGS FOUND
        		-0.47 -2.59 0.42 4.70 3.99 0.60 -3.09
        4
        		 -0.02 -0.05 0.00 0.04 0.07 0.02 -0.04
        GM.5.0.Forkhead.0042
        FOXH1
        		-0.98 -1.56 -1.06 1.47 3.80 2.57 -2.30
        3
        		 -0.01 -0.03 -0.03 -0.01 0.03 0.05 0.00
        GM.5.0.E2F.0002
        E2F7,TFDP2,E2F4,TFDP1B,E2F1, (...)
        		-2.48 1.20 1.01 -1.83 -3.81 1.22 1.60
        1
        		 -0.09 -0.05 0.00 -0.01 -0.02 0.05 0.10
        GM.5.0.Nuclear_receptor.0148
        NR1H4,NO ORTHOLOGS FOUND
        		2.19 0.32 2.21 2.68 1.96 -0.61 -3.31
        <1
        		 0.00 -0.01 0.01 0.02 0.05 -0.00 -0.05
        GM.5.0.C2H2_ZF.0126
        LOC563292,ZFX,ZNF711
        		1.67 3.79 0.48 -0.95 -1.78 -3.55 0.53
        1
        		 0.01 0.01 -0.00 -0.03 -0.02 -0.04 0.05
        GM.5.0.IRF.0008
        IRF6,IRF5,IRF10,IRF4A,IRF2A, (...)
        		-2.41 -0.14 3.54 2.12 1.55 -1.21 -1.13
        1
        		 -0.08 -0.08 0.01 0.04 0.02 0.03 0.06
        GM.5.0.SAND.0005
        ARHGEF12B,NO ORTHOLOGS FOUND,ARHGEF12A
        		-3.21 -1.03 3.23 1.82 0.48 -0.26 0.14
        <1
        		 -0.08 -0.07 0.06 0.07 0.04 0.02 0.01
        GM.5.0.Sox.0033
        SOX3,LOC110439851,SOX1A,SOX1B,SOX8A, (...)
        		-1.23 -3.62 -1.87 1.04 3.02 2.85 1.83
        <1
        		 -0.03 -0.05 -0.01 0.00 0.03 0.05 0.01
        GM.5.0.Nuclear_receptor.0147
        ESRRA,PPARGC1A,ESRRGA,ESRRGB,ESRRB
        		1.50 2.51 1.55 0.20 -0.53 -1.38 -3.14
        <1
        		 0.01 0.01 0.02 0.01 0.03 -0.02 -0.03
        GM.5.0.Ets.0037
        GABPA,NELFE,RAD21B,MYCB,HDAC1, (...)
        		-3.41 -3.46 -2.04 0.60 -0.91 3.33 2.64
        1
        		 -0.09 -0.09 -0.06 -0.04 -0.04 0.07 0.17
        GM.5.0.C2H2_ZF.0257
        KLF5L,KLF5A,KLF2A,KLF2B,KLF5B, (...)
        		1.73 -0.78 -2.51 -4.04 -1.54 0.70 1.11
        2
        		 0.00 -0.01 -0.06 -0.05 0.00 0.05 0.04
        GM.5.0.C2H2_ZF.0205
        AHR1B,AHRRB,AHR1A,ARNT2,AHR2, (...)
        		-2.46 -2.32 -2.63 0.51 2.61 4.44 -0.86
        <1
        		 -0.02 -0.04 -0.04 0.01 0.03 0.09 -0.02
        GM.5.0.bHLH.0089
        LOC101883970,TAL1,ATOH7,NEUROD4,TCF12, (...)
        		0.13 -1.06 -1.84 -2.80 -0.60 0.28 3.20
        <1
        		 0.01 -0.02 -0.04 -0.05 0.01 0.03 0.04
        GM.5.0.Paired_box.0013
        PAX8,PAX9,PAX1A,PAX1B,PAX5
        		-3.15 0.51 -1.45 0.72 0.62 0.06 2.48
        <1
        		 -0.01 -0.00 -0.03 -0.02 0.01 0.01 0.03
        GM.5.0.bHLH.0076
        HEYL,HEY1,HEY2
        		3.60 0.94 0.57 0.05 -2.03 -1.55 -2.69
        <1
        		 0.01 -0.00 0.00 -0.01 -0.01 0.02 -0.01
        GM.5.0.Mixed.0007
        RAD21L1,LOC110439851,SMC3,RAD21B,RAD21A, (...)
        		3.78 3.25 2.01 -0.34 0.63 -2.75 -2.75
        <1
        		 0.04 0.03 -0.01 -0.03 0.00 -0.02 -0.02
        GM.5.0.C2H2_ZF.0273
        NR2E3,NO ORTHOLOGS FOUND
        		-3.48 -1.96 -1.21 1.09 1.10 2.12 2.75
        1
        		 -0.05 -0.06 -0.01 0.01 0.02 0.02 0.06
        GM.5.0.C2H2_ZF.0174
        ZGC_77358,SP8B,KLF7A,SP8A,SP2, (...)
        		-2.21 0.75 3.56 2.73 1.24 -1.03 -0.51
        <1
        		 -0.09 -0.03 0.04 0.04 0.02 0.03 0.02
        GM.5.0.bHLH.0072
        OSR2,MYOD1,NO ORTHOLOGS FOUND,MYOG,MYF5, (...)
        		-0.08 -2.93 -2.69 -2.77 -1.66 1.67 4.01
        2
        		 -0.01 -0.03 -0.06 -0.07 -0.02 0.05 0.08
        GM.5.0.p53.0010
        TP53,TP63,TP73
        		0.88 3.33 0.96 0.79 -1.93 -1.71 -0.44
        1
        		 0.01 0.01 0.01 0.01 -0.00 -0.02 -0.01
        GM.5.0.Mixed.0037
        CHD2,CHD1,LOC110438533,SP1,E2F1
        		-2.31 -3.19 1.43 0.56 1.46 1.33 1.09
        2
        		 -0.08 -0.09 0.02 0.04 0.04 0.05 0.04
        GM.5.0.Homeodomain.0030
        HOXA9A,HOXD9A,HOXB10A,HOXA9B,HOXC9A, (...)
        		-2.91 -2.79 -1.16 1.12 0.91 -0.12 4.00
        1
        		 -0.04 -0.06 0.01 0.02 0.04 0.02 0.03
        GM.5.0.Forkhead.0058
        FOXD5,FOXI3A,FOXQ1B,FOXI3B,FOXD3, (...)
        		-1.96 -1.78 -3.31 0.69 1.64 1.78 -0.44
        1
        		 -0.01 -0.02 -0.04 -0.01 0.02 0.04 0.00
        GM.5.0.Homeodomain.0155
        SOX14,CUX1A,MEOX2B,SOX21B,CUX1B, (...)
        		3.29 2.79 2.70 -3.06 -2.57 -1.31 -1.67
        1
        		 0.02 0.01 0.00 -0.03 -0.00 0.02 -0.02
        GM.5.0.bHLH.0102
        MYOD1,TFAP4,MYF5,FERD3L,PTF1A, (...)
        		1.80 3.26 -0.42 -1.40 -2.99 -2.67 0.17
        1
        		 0.04 0.00 -0.02 -0.04 -0.03 -0.00 0.02
        GM.5.0.Unknown.0018
        NO ORTHOLOGS FOUND
        		-0.84 -1.33 -2.56 -2.29 -0.87 3.03 3.65
        1
        		 -0.04 -0.04 -0.04 -0.04 -0.02 0.05 0.09
        GM.5.0.Unknown.0001
        RAD21L1,RAD21B,SMC3,RAD21A
        		0.91 3.96 -1.90 -1.46 -1.76 -1.14 -0.71
        2
        		 -0.00 0.01 -0.01 -0.02 0.03 0.00 -0.01
        GM.5.0.Nuclear_receptor.0035
        RXRBB,RXRGB,RXRAB,RXRGA,RXRBA, (...)
        		2.00 -0.17 -2.02 -1.58 -3.51 -1.86 1.49
        <1
        		 0.02 0.01 -0.03 -0.05 -0.02 -0.01 0.04
        GM.5.0.T-box.0013
        ZEB2A,ZEB1B,ZEB2B,TBX3A
        		5.58 1.96 0.43 -0.21 -0.98 -2.65 -1.48
        4
        		 0.05 0.01 -0.03 -0.05 -0.00 0.01 -0.01
        GM.5.0.Homeodomain.0097
        DRGX,OTPB,OTPA,ALX1,VSX2, (...)
        		-2.15 -2.65 -2.15 -1.18 0.59 0.79 3.53
        1
        		 -0.03 -0.05 -0.00 0.01 0.02 0.01 0.04
        GM.5.0.Homeodomain.0027
        PBX1B,PBX3B,PBX4,PBX2,PBX1A, (...)
        		1.41 3.34 -0.17 -0.86 0.65 0.77 -3.22
        1
        		 -0.01 0.02 0.02 -0.01 0.02 0.00 -0.03
        GM.5.0.Grainyhead.0010
        GRHL1,GRHL2A,GRHL2B,GRHL3,UBP1, (...)
        		3.52 -0.60 0.12 2.84 1.85 -2.09 -2.68
        2
        		 -0.00 -0.03 0.02 0.05 0.04 -0.01 -0.03
        GM.5.0.T-box.0007
        LOC100330653,TBX1
        		2.24 0.23 2.09 -0.69 2.92 -0.28 -4.55
        1
        		 0.01 -0.02 -0.00 -0.01 0.03 0.02 -0.02
        GM.5.0.Unknown.0152
        FOXA1,FOXA2,LOC100149117,FOXL1,FOXA3, (...)
        		-2.57 -2.01 -1.99 -1.58 0.16 2.25 3.04
        1
        		 -0.04 -0.04 -0.05 -0.04 -0.01 0.07 0.07
        GM.5.0.Myb_SANT.0008
        MYB,SI_DKEY-17E16.13,ZGC_171929,MYBL2B,MYBL1, (...)
        		-1.24 -1.28 2.09 3.08 2.66 0.49 -2.30
        <1
        		 -0.04 -0.04 0.03 0.05 0.05 0.01 -0.02
        GM.5.0.C2H2_ZF.0073
        ETS1,ZNF143A,ZNF143B
        		-1.07 -0.46 -1.11 -3.40 -3.30 1.60 1.21
        1
        		 -0.04 -0.02 -0.01 -0.04 -0.04 0.02 0.09
        GM.5.0.Forkhead.0050
        FOXD5,FOXI3A,FOXQ1B,FOXI3B,FOXD3, (...)
        		-1.23 -3.07 -3.67 -1.25 1.65 1.30 3.80
        1
        		 -0.03 -0.06 -0.05 -0.03 0.01 0.05 0.08
        GM.5.0.AP-2.0001
        TFAP2A,TFAP2E,TFAP2D,TFAP2C,TFAP2B, (...)
        		2.29 -2.92 -4.49 -4.78 -4.54 -4.64 5.99
        <1
        		 0.01 -0.03 -0.05 -0.07 -0.03 -0.03 0.13
        GM.5.0.Homeodomain.0056
        LOC100535338,TGIF1,MEIS1A,MEIS3,MEIS2B, (...)
        		3.54 0.35 -0.15 -2.49 -0.91 -0.28 1.07
        1
        		 0.03 -0.01 -0.02 -0.04 -0.00 0.01 0.01
        GM.5.0.Homeodomain.0099
        ISL2A,ISL2B,PDX1,ISL1
        		-1.28 -2.74 0.04 2.17 3.55 2.98 -3.63
        3
        		 -0.01 -0.05 0.00 0.03 0.08 0.04 -0.06
        GM.5.0.Forkhead.0019
        SI_DKEY-11F5.5,FOXO3A,SI_CH211-206A7.2,FOXO3B,FOXO4, (...)
        		0.09 -1.52 -1.86 -1.85 -1.56 2.17 3.20
        <1
        		 -0.04 -0.06 -0.04 -0.04 -0.00 0.07 0.08
        GM.5.0.C2H2_ZF.0029
        ZBTB14,NO ORTHOLOGS FOUND,SI_CH211-160F23.5,E2F3,E2F1
        		-1.09 -4.21 0.30 3.34 3.63 3.14 -2.96
        <1
        		 -0.05 -0.06 0.04 0.07 0.06 0.06 -0.06
        GM.5.0.Homeodomain.0062
        PITX3,PITX2,PITX1,DRGX,CRX, (...)
        		2.28 1.02 -2.04 -1.04 -2.72 -4.73 3.95
        2
        		 0.00 -0.03 -0.03 -0.02 -0.02 -0.03 0.08
        GM.5.0.T-box.0014
        MGAA,TBX2B,TBX5A,TBX5B,TBX2A, (...)
        		-0.09 -2.42 -3.40 -3.96 2.77 4.34 0.06
        2
        		 0.00 -0.04 -0.03 -0.03 0.05 0.06 -0.02
        GM.5.0.Homeodomain.0063
        GBX2,EN1A,EMX2,EMX3,GBX1, (...)
        		-1.99 0.05 2.16 1.91 3.93 -2.01 -1.85
        1
        		 -0.02 -0.02 0.03 0.04 0.07 0.00 -0.05
        GM.5.0.Sox.0029
        TCF7L1A,TCF7L2,TCF7,TCF7L1B,LEF1, (...)
        		-0.86 -2.72 -3.15 -1.06 0.16 0.60 2.62
        3
        		 -0.06 -0.08 -0.03 -0.00 0.02 0.03 0.09
        GM.5.0.Ets.0026
        ERG,EHF,FEV,ERFL3,FLI1A, (...)
        		-2.24 -2.11 2.62 3.69 3.22 1.22 -1.28
        1
        		 -0.07 -0.08 0.01 0.04 0.04 0.05 0.03
        GM.5.0.C2H2_ZF.0190
        EGR1,EGR2B,EGR2A,EGR3,EGR4, (...)
        		-3.35 -0.59 -3.42 -2.28 -1.08 3.76 2.62
        2
        		 -0.06 -0.01 -0.08 -0.04 -0.05 0.08 0.11
        GM.5.0.T-box.0002
        TB,TBX19,TA,EOMESB,TBR1A, (...)
        		3.15 -0.58 -2.58 -4.17 -2.50 2.69 2.47
        2
        		 0.04 -0.02 -0.05 -0.07 -0.01 0.04 0.03
        GM.5.0.Sox.0002
        SOX18,SOX17,SOX5,SOX8A,SOX6, (...)
        		-3.71 -3.45 -2.81 2.80 3.18 1.76 2.65
        2
        		 -0.08 -0.11 -0.03 0.02 0.04 0.05 0.09
        GM.5.0.IRF.0011
        NO ORTHOLOGS FOUND,IRF4B,BCL11BA,IM_7142702,IRF8, (...)
        		-2.63 -2.45 -3.88 -3.46 -3.86 3.47 4.52
        2
        		 -0.08 -0.07 -0.09 -0.06 -0.08 0.07 0.21
        GM.5.0.C2H2_ZF.0031
        PBX2,PBX3B,PBX4,PBX1A,PBX3A, (...)
        		-4.62 -0.59 3.02 1.90 1.67 -0.10 0.98
        2
        		 -0.06 -0.01 0.03 0.02 0.02 0.01 0.02
        GM.5.0.GATA.0005
        GATA3,GATA1A,GATA2A,GATA1B,GATA6, (...)
        		-0.74 -2.19 -4.34 -2.99 -0.73 1.64 4.36
        <1
        		 -0.01 -0.04 -0.05 -0.04 -0.01 0.02 0.09
        GM.5.0.Sox.0019
        SOX8A,SOX10,SOX9A,SOX3,SOX1A, (...)
        		-4.26 -4.67 -2.92 2.33 3.49 4.32 3.52
        3
        		 -0.08 -0.12 -0.05 0.01 0.03 0.07 0.11
        GM.5.0.Homeodomain.0167
        HMX1,MSX2A,MSX1A,NO ORTHOLOGS FOUND,BARHL2, (...)
        		0.81 1.36 3.30 5.24 5.01 -0.55 -4.89
        2
        		 -0.00 0.01 0.03 0.03 0.08 -0.00 -0.08
        GM.5.0.C2H2_ZF.0268
        KLF5L,KLF5A,KLF2A,KLF2B,KLF5B, (...)
        		1.36 1.05 0.62 1.85 -2.31 -3.91 -0.21
        2
        		 -0.02 0.01 -0.01 0.00 -0.02 -0.01 0.03
        GM.5.0.Nuclear_receptor.0104
        RXRBA,RXRGA,RXRBB,RXRAA,RXRAB, (...)
        		-4.16 -2.65 0.90 2.08 3.43 1.70 1.61
        2
        		 -0.10 -0.06 0.02 0.05 0.07 0.05 0.02
        GM.5.0.bZIP.0016
        CREMB,CREB1A,ATF1,CREB1B,CREMA, (...)
        		-3.35 -0.50 2.37 3.00 0.93 -0.28 -0.22
        3
        		 -0.05 -0.02 0.06 0.05 0.03 0.01 -0.03
        GM.5.0.Forkhead.0008
        FOXA1,FOXA2,FOXA3,FOXD5,FOXQ1B, (...)
        		-0.49 -1.23 -2.15 -4.84 0.54 2.32 4.23
        2
        		 -0.03 -0.06 -0.05 -0.05 0.01 0.07 0.07
        GM.5.0.C2H2_ZF.0108
        ZIC3,LOC110438163,ZIC4,ZIC1,ZIC6, (...)
        		-3.74 -6.14 -5.63 -5.99 2.01 6.14 5.69
        3
        		 -0.06 -0.08 -0.11 -0.09 0.04 0.13 0.12
        GM.5.0.T-box.0008
        TBX5A,LOC100330653,TBX5B,TBX1,TBX20, (...)
        		3.17 -0.56 -0.21 -0.99 3.12 2.70 -4.06
        2
        		 0.05 -0.00 -0.03 -0.05 0.02 0.03 -0.03
        GM.5.0.TEA.0007
        TEAD3B,TEAD1B,TEAD1A,TEAD3A,BCL11AB, (...)
        		0.35 -1.57 -0.43 -0.20 -1.94 -1.90 3.26
        2
        		 -0.02 -0.04 -0.01 -0.00 -0.00 0.00 0.05
        GM.5.0.Rel.0018
        NO ORTHOLOGS FOUND,TAF1,ERG,FLI1A,EWSR1A, (...)
        		2.04 1.22 -4.48 -5.39 -5.24 1.15 4.70
        2
        		 -0.04 -0.03 -0.09 -0.09 -0.11 0.04 0.21
        GM.5.0.Nuclear_receptor.0013
        HNF4A,PPARDB,PPARG,PPARAA,PPARAB, (...)
        		-0.56 2.10 -3.12 -3.80 -1.97 1.38 2.17
        2
        		 0.01 0.00 -0.02 -0.04 -0.02 -0.01 0.05
        GM.5.0.C2H2_ZF.0072
        ZGC_77358,SP8B,SP8A,SP9,SP2, (...)
        		-1.77 2.52 5.54 3.56 1.10 -1.52 -2.71
        2
        		 -0.09 -0.01 0.05 0.04 0.02 0.03 0.01
        GM.5.0.C2H2_ZF.0254
        RAD21L1,RAD21B,CTCF,RAD21A
        		-1.32 -2.23 -0.40 2.08 3.39 1.24 -0.82
        2
        		 -0.03 -0.02 0.00 0.03 0.06 0.00 -0.02
        GM.5.0.Mixed.0079
        CTCF,RAD21L1,SMC3,RAD21B,RAD21A
        		-3.50 -1.33 -0.34 2.01 1.35 1.43 0.41
        2
        		 -0.07 -0.05 -0.00 0.02 0.06 0.04 0.02
        GM.5.0.Homeodomain_POU.0012
        POU2F1A,POU2F1B,POU3F3A,POU5F3,POU3F2B, (...)
        		-1.72 -4.12 3.37 4.11 3.42 4.13 -4.23
        3
        		 -0.02 -0.08 0.02 0.05 0.07 0.07 -0.06
        GM.5.0.GATA.0010
        NO ORTHOLOGS FOUND,GATA1B,GATA1A,RREB1A,GATA3, (...)
        		-2.27 -1.55 -5.54 -0.78 -0.13 5.32 4.45
        4
        		 0.00 0.01 -0.11 -0.04 -0.03 0.09 0.03
        GM.5.0.Unknown.0081
        NO ORTHOLOGS FOUND,ZGC_77358,WT1B,RXRBB,MYCB, (...)
        		-4.59 -1.76 1.22 4.15 2.25 3.70 -3.13
        3
        		 -0.08 -0.02 -0.01 0.00 -0.02 0.04 0.08
        GM.5.0.Homeodomain_POU.0007
        NO ORTHOLOGS FOUND,SOX3,SOX1A,SOX2,SOX1B, (...)
        		-4.37 -5.01 -0.52 3.44 4.00 4.01 -0.36
        4
        		 -0.05 -0.09 -0.01 0.02 0.06 0.08 0.00
        GM.5.0.C2H2_ZF.0061
        NO ORTHOLOGS FOUND,VEZF1B,LOC100535691,SI_CH211-166G5.4,VEZF1A, (...)
        		-5.08 -4.44 -3.24 0.15 1.68 4.63 4.62
        3
        		 -0.10 -0.05 -0.05 -0.02 -0.02 0.06 0.13
        GM.5.0.Unknown.0182
        NFYC,NFYBA,NFYBB,NFYAL,PBX1B, (...)
        		-5.54 2.60 3.23 2.72 1.29 2.71 0.05
        3
        		 -0.07 0.03 0.06 0.03 0.03 -0.01 -0.02
        GM.5.0.C2H2_ZF.0023
        CTCF,RAD21B,RAD21A,RAD21L1,SMC3, (...)
        		-5.91 -5.05 0.96 5.06 6.14 4.89 -2.56
        5
        		 -0.10 -0.06 -0.01 0.04 0.13 0.07 -0.01

        Samples & Config

        The samples file used for this run:

        sample assembly biological_replicates descriptive_name
        GSM3756599 danRer11 256cell 256-cell-rep1
        GSM3756600 danRer11 256cell 256-cell-rep2
        GSM3756606 danRer11 high High-rep1
        GSM3756607 danRer11 high High-rep2
        GSM3756608 danRer11 high High-rep3
        GSM3756609 danRer11 oblong Oblong-rep1
        GSM3756610 danRer11 oblong Oblong-rep2
        GSM3756611 danRer11 oblong Oblong-rep3
        GSM3756614 danRer11 sphere Sphere-rep1
        GSM3756615 danRer11 sphere Sphere-rep2
        GSM3756603 danRer11 dome Dome-rep1
        GSM3756604 danRer11 dome Dome-rep2
        GSM3756605 danRer11 dome Dome-rep3
        GSM3756612 danRer11 shield Shield-rep1
        GSM3756613 danRer11 shield Shield-rep2
        GSM3756601 danRer11 80epiboly 80epiboly-rep1
        GSM3756602 danRer11 80epiboly 80epiboly-rep2

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

# pipeline file locations
result_dir: ./results  # where to store results
genome_dir: ./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: yourmail@here.com

# 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

# whether or not to run gimme maelstrom to infer differential motifs
run_gimme_maelstrom: true

# differential accessibility analysis
# for explanation, see: https://vanheeringen-lab.github.io/seq2science/content/DESeq2.html
contrasts:
  - 'biological_replicates_80epiboly_256cell'

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

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