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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 1.14

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

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        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 v1.2.0, 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
        October 05, 2023
        Project
        2023_s2s_run
        Contact E-mail
        slrinzema@science.ru.nl

        Report generated on 2023-10-06, 04:27 CEST based on data in:

        Change sample names:

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        General Statistics

        Showing 105/105 rows and 12/22 columns.
        Sample Name% DuplicationM Reads After FilteringGC content% PF% AdapterInsert Size% Dups% MappedM Total seqsGenome coverageM Genome readsM MT genome reads
        D10_supernatant_DMSO_1
        23.0%
        40.7
        49.8%
        100.0%
        0.0%
        237 bp
        27.7%
        100.0%
        39.5
        0.9 X
        63.7
        0.9
        D10_supernatant_DMSO_2
        31.5%
        45.4
        51.2%
        100.0%
        0.0%
        210 bp
        39.2%
        100.0%
        43.9
        1.0 X
        73.5
        0.7
        D10_supernatant_DMSO_3
        26.6%
        61.7
        53.4%
        100.0%
        0.0%
        195 bp
        33.5%
        100.0%
        59.1
        1.4 X
        106.5
        2.2
        D10_supernatant_TA_1
        32.5%
        41.8
        51.1%
        100.0%
        0.0%
        238 bp
        39.0%
        100.0%
        40.6
        1.5 X
        107.5
        0.7
        D10_supernatant_TA_2
        46.2%
        73.9
        52.6%
        100.0%
        0.0%
        195 bp
        56.0%
        100.0%
        71.6
        1.7 X
        127.0
        1.4
        D10_supernatant_TA_3
        32.3%
        78.8
        55.1%
        100.0%
        0.0%
        176 bp
        40.3%
        100.0%
        75.6
        2.0 X
        147.1
        2.6
        D12_adherent_DMSO_1
        14.4%
        63.6
        49.3%
        100.0%
        0.0%
        255 bp
        17.7%
        100.0%
        61.8
        1.2 X
        85.8
        1.4
        D12_adherent_DMSO_2
        54.0%
        45.2
        51.9%
        100.0%
        0.0%
        218 bp
        17.4%
        100.0%
        15.7
        0.3 X
        25.8
        0.6
        D12_adherent_DMSO_3
        24.5%
        56.5
        53.9%
        100.0%
        0.0%
        197 bp
        27.4%
        100.0%
        51.7
        1.1 X
        82.0
        0.4
        D12_adherent_TA_1
        13.9%
        42.0
        47.6%
        100.0%
        0.0%
        271 bp
        16.9%
        100.0%
        40.7
        0.7 X
        51.8
        1.3
        D12_adherent_TA_2
        51.1%
        49.7
        51.4%
        100.0%
        0.0%
        204 bp
        15.8%
        100.0%
        18.9
        0.4 X
        29.0
        0.7
        D12_adherent_TA_3
        14.1%
        50.6
        50.3%
        100.0%
        0.0%
        203 bp
        17.7%
        100.0%
        49.0
        0.9 X
        66.9
        0.7
        D12_supernatant_DMSO_1
        17.8%
        96.1
        49.0%
        100.0%
        0.0%
        234 bp
        21.4%
        100.0%
        93.6
        1.8 X
        133.1
        3.2
        D12_supernatant_DMSO_2
        18.1%
        98.2
        50.2%
        100.0%
        0.0%
        207 bp
        22.1%
        100.0%
        95.2
        1.9 X
        137.3
        3.0
        D12_supernatant_DMSO_3
        40.0%
        85.4
        51.4%
        100.0%
        0.0%
        194 bp
        15.1%
        100.0%
        44.5
        0.8 X
        59.0
        1.6
        D12_supernatant_RU1uMTA100nM_1
        9.3%
        30.5
        48.7%
        100.0%
        0.0%
        202 bp
        11.6%
        100.0%
        29.4
        0.6 X
        40.7
        0.9
        D12_supernatant_RU1uMTA100nM_2
        14.2%
        43.1
        51.4%
        100.0%
        0.0%
        203 bp
        17.8%
        100.0%
        41.9
        0.8 X
        60.2
        1.7
        D12_supernatant_RU1uMTA100nM_3
        12.9%
        44.8
        50.0%
        100.0%
        0.0%
        218 bp
        15.8%
        100.0%
        43.2
        0.8 X
        60.1
        1.8
        D12_supernatant_RU1uMTA1uM_1
        11.9%
        41.5
        48.8%
        100.0%
        0.0%
        219 bp
        14.7%
        100.0%
        39.8
        0.7 X
        55.2
        1.6
        D12_supernatant_RU1uMTA1uM_2
        10.9%
        34.4
        50.0%
        100.0%
        0.0%
        219 bp
        13.9%
        100.0%
        33.3
        0.6 X
        46.9
        1.3
        D12_supernatant_RU1uMTA1uM_3
        14.1%
        44.9
        51.1%
        100.0%
        0.0%
        203 bp
        17.3%
        100.0%
        43.5
        0.9 X
        63.4
        1.9
        D12_supernatant_RU1uM_1
        12.5%
        31.4
        50.3%
        100.0%
        0.0%
        227 bp
        15.4%
        100.0%
        30.4
        0.6 X
        44.6
        1.1
        D12_supernatant_RU1uM_2
        10.8%
        42.0
        50.3%
        100.0%
        0.0%
        226 bp
        13.9%
        100.0%
        40.5
        0.8 X
        57.8
        1.5
        D12_supernatant_RU1uM_3
        12.9%
        36.2
        50.4%
        100.0%
        0.0%
        210 bp
        15.9%
        100.0%
        35.0
        0.7 X
        49.1
        1.6
        D12_supernatant_TA100nM_1
        12.2%
        32.0
        51.3%
        100.0%
        0.0%
        173 bp
        15.3%
        100.0%
        31.1
        0.6 X
        46.5
        1.4
        D12_supernatant_TA100nM_2
        12.1%
        36.8
        50.7%
        100.0%
        0.0%
        224 bp
        15.3%
        100.0%
        35.7
        0.7 X
        53.0
        1.1
        D12_supernatant_TA100nM_3
        15.0%
        44.3
        50.1%
        100.0%
        0.0%
        176 bp
        18.6%
        100.0%
        43.0
        0.8 X
        60.3
        2.0
        D12_supernatant_TA1uM_1
        12.5%
        36.3
        50.2%
        100.0%
        0.0%
        198 bp
        15.4%
        100.0%
        35.3
        0.7 X
        51.5
        1.3
        D12_supernatant_TA1uM_2
        11.1%
        37.5
        51.5%
        100.0%
        0.0%
        223 bp
        14.3%
        100.0%
        36.3
        0.7 X
        54.3
        1.2
        D12_supernatant_TA1uM_3
        13.1%
        38.7
        49.2%
        100.0%
        0.0%
        226 bp
        16.1%
        100.0%
        37.8
        0.7 X
        51.7
        1.6
        D12_supernatant_TA_1
        13.4%
        40.1
        48.1%
        100.0%
        0.0%
        253 bp
        16.4%
        100.0%
        38.9
        0.7 X
        53.7
        1.1
        D12_supernatant_TA_2
        15.6%
        49.7
        52.0%
        100.0%
        0.0%
        208 bp
        20.4%
        100.0%
        48.2
        1.1 X
        78.2
        1.5
        D12_supernatant_TA_3
        55.4%
        51.4
        53.3%
        100.0%
        0.0%
        224 bp
        11.7%
        100.0%
        13.5
        0.3 X
        19.3
        0.5
        D18_adherent_DMSO_2
        28.6%
        68.0
        55.7%
        100.0%
        0.0%
        171 bp
        35.8%
        100.0%
        66.2
        1.6 X
        117.2
        0.7
        D18_adherent_DMSO_3
        73.0%
        22.7
        49.7%
        100.0%
        0.0%
        178 bp
        83.6%
        100.0%
        21.4
        0.3 X
        25.1
        0.2
        D18_adherent_TA_2
        53.4%
        124.3
        55.7%
        100.0%
        0.0%
        189 bp
        63.1%
        100.0%
        120.5
        3.2 X
        234.9
        0.9
        D18_adherent_TA_3
        21.9%
        57.1
        51.9%
        100.0%
        0.0%
        223 bp
        26.5%
        100.0%
        55.5
        1.0 X
        76.1
        0.6
        D18_supernatant_DMSO_2
        9.8%
        50.8
        49.1%
        100.0%
        0.0%
        224 bp
        12.7%
        100.0%
        48.7
        0.9 X
        67.3
        1.1
        D18_supernatant_DMSO_3
        10.2%
        53.8
        48.1%
        100.0%
        0.0%
        214 bp
        12.8%
        100.0%
        51.8
        0.9 X
        65.2
        1.3
        D18_supernatant_TA_2
        10.9%
        51.8
        49.9%
        100.0%
        0.0%
        209 bp
        14.4%
        100.0%
        49.5
        1.0 X
        70.6
        1.2
        D18_supernatant_TA_3
        13.3%
        57.2
        50.0%
        100.0%
        0.0%
        203 bp
        16.8%
        100.0%
        55.1
        1.0 X
        71.5
        1.3
        D19_adherent_DMSO_1
        37.4%
        44.1
        51.7%
        100.0%
        0.0%
        223 bp
        44.5%
        100.0%
        42.8
        1.4 X
        100.5
        0.7
        D19_adherent_TA_1
        33.8%
        37.2
        50.5%
        100.0%
        0.0%
        194 bp
        39.2%
        100.0%
        36.1
        0.6 X
        46.5
        0.4
        D19_supernatant_DMSO_1
        10.8%
        46.6
        48.9%
        100.0%
        0.0%
        209 bp
        13.0%
        100.0%
        45.0
        0.8 X
        60.1
        0.8
        D19_supernatant_TA_1
        14.9%
        43.1
        49.7%
        100.0%
        0.0%
        246 bp
        18.2%
        100.0%
        41.8
        0.8 X
        62.3
        0.8
        D1_adherent_TA_1
        14.1%
        48.5
        49.9%
        100.0%
        0.0%
        250 bp
        17.4%
        100.0%
        46.4
        1.0 X
        75.2
        0.7
        D1_adherent_TA_2
        21.8%
        52.4
        54.9%
        100.0%
        0.0%
        235 bp
        29.1%
        100.0%
        50.3
        1.4 X
        104.1
        0.7
        D1_adherent_TA_3
        17.8%
        52.7
        49.6%
        100.0%
        0.0%
        225 bp
        22.1%
        100.0%
        50.8
        1.1 X
        78.8
        0.4
        D1_adherent_TA_DMSO_1
        20.3%
        49.7
        51.2%
        100.0%
        0.0%
        260 bp
        25.4%
        100.0%
        47.9
        1.6 X
        118.6
        0.9
        D1_adherent_TA_DMSO_2
        20.7%
        48.1
        54.6%
        100.0%
        0.0%
        222 bp
        27.6%
        100.0%
        46.3
        1.2 X
        92.5
        0.6
        D1_adherent_TA_DMSO_3
        28.8%
        52.7
        53.4%
        100.0%
        0.0%
        203 bp
        35.1%
        100.0%
        51.0
        1.2 X
        91.7
        0.5
        HSCD12_DMSO_1bio
        12.6%
        50.4
        49.0%
        97.1%
        0.0%
        HSCD12_DMSO_2bio
        19.2%
        49.9
        51.2%
        96.8%
        0.1%
        HSCD12_DMSO_3bio
        11.1%
        35.6
        48.4%
        96.4%
        0.1%
        HSCD12_RU1uMTA100nM_1bio
        9.1%
        30.5
        48.7%
        96.9%
        0.1%
        HSCD12_RU1uMTA100nM_2bio
        13.7%
        43.1
        51.4%
        95.6%
        0.1%
        HSCD12_RU1uMTA100nM_3bio
        12.7%
        44.8
        50.0%
        97.3%
        0.1%
        HSCD12_RU1uMTA1uM_1bio
        11.6%
        41.5
        48.8%
        96.3%
        0.1%
        HSCD12_RU1uMTA1uM_2bio
        10.8%
        34.4
        50.0%
        97.9%
        0.1%
        HSCD12_RU1uMTA1uM_3bio
        13.8%
        44.9
        51.1%
        97.7%
        0.1%
        HSCD12_RU1uM_1bio
        12.3%
        31.4
        50.3%
        97.2%
        0.0%
        HSCD12_RU1uM_2bio
        10.5%
        42.0
        50.3%
        96.5%
        0.1%
        HSCD12_RU1uM_3bio
        12.6%
        36.2
        50.4%
        96.7%
        0.1%
        HSCD12_TA100nM_1bio
        12.0%
        32.0
        51.3%
        97.7%
        0.1%
        HSCD12_TA100nM_2bio
        11.7%
        36.8
        50.7%
        95.6%
        0.1%
        HSCD12_TA100nM_3bio
        14.6%
        44.3
        50.1%
        96.4%
        0.2%
        HSCD12_TA1uM_1bio
        12.3%
        36.3
        50.2%
        97.1%
        0.1%
        HSCD12_TA1uM_2bio
        10.9%
        37.5
        51.5%
        97.4%
        0.0%
        HSCD12_TA1uM_3bio
        13.0%
        38.7
        49.2%
        98.3%
        0.1%
        NP_Day10_supernatant_DMSO_1
        22.3%
        40.7
        49.8%
        95.9%
        0.0%
        NP_Day10_supernatant_DMSO_2
        30.5%
        45.4
        51.2%
        95.8%
        0.0%
        NP_Day10_supernatant_DMSO_3
        25.8%
        61.7
        53.4%
        96.5%
        0.0%
        NP_Day10_supernatant_TA_1
        31.3%
        41.8
        51.1%
        95.0%
        0.0%
        NP_Day10_supernatant_TA_2
        44.5%
        73.9
        52.6%
        95.4%
        0.0%
        NP_Day10_supernatant_TA_3
        31.3%
        78.8
        55.1%
        96.0%
        0.1%
        NP_Day12_adherent_DMSO_1
        14.1%
        63.6
        49.3%
        97.5%
        0.0%
        NP_Day12_adherent_DMSO_2
        52.9%
        45.2
        51.9%
        97.6%
        0.0%
        NP_Day12_adherent_DMSO_3
        23.9%
        56.5
        53.9%
        97.0%
        0.0%
        NP_Day12_adherent_TA_1
        13.6%
        42.0
        47.6%
        96.6%
        0.1%
        NP_Day12_adherent_TA_2
        50.2%
        49.7
        51.4%
        98.0%
        0.0%
        NP_Day12_adherent_TA_3
        13.8%
        50.6
        50.3%
        97.2%
        0.0%
        NP_Day12_supernatant_DMSO_1
        17.9%
        45.8
        48.9%
        97.5%
        0.0%
        NP_Day12_supernatant_DMSO_2
        11.2%
        48.3
        49.1%
        97.5%
        0.1%
        NP_Day12_supernatant_DMSO_3
        57.7%
        49.8
        53.5%
        97.4%
        0.0%
        NP_Day12_supernatant_TA_1
        13.1%
        40.1
        48.1%
        97.0%
        0.0%
        NP_Day12_supernatant_TA_2
        15.2%
        49.7
        52.0%
        96.2%
        0.0%
        NP_Day12_supernatant_TA_3
        54.8%
        51.4
        53.3%
        98.5%
        0.0%
        NP_Day18_adherent_DMSO_2
        27.6%
        68.0
        55.7%
        95.7%
        0.1%
        NP_Day18_adherent_DMSO_3
        70.7%
        22.7
        49.7%
        96.2%
        0.1%
        NP_Day18_adherent_TA_2
        51.7%
        124.3
        55.7%
        95.9%
        0.0%
        NP_Day18_adherent_TA_3
        21.5%
        57.1
        51.9%
        97.8%
        0.0%
        NP_Day18_supernatant_DMSO_2
        9.7%
        50.8
        49.1%
        97.6%
        0.1%
        NP_Day18_supernatant_DMSO_3
        10.0%
        53.8
        48.1%
        97.9%
        0.0%
        NP_Day18_supernatant_TA_2
        10.7%
        51.8
        49.9%
        97.1%
        0.0%
        NP_Day18_supernatant_TA_3
        13.0%
        57.2
        50.0%
        97.7%
        0.0%
        NP_Day19_adherent_DMSO_1
        36.1%
        44.1
        51.7%
        95.7%
        0.0%
        NP_Day19_adherent_TA_1
        32.8%
        37.2
        50.5%
        96.2%
        0.1%
        NP_Day19_supernatant_DMSO_1
        10.5%
        46.6
        48.9%
        96.8%
        0.1%
        NP_Day19_supernatant_TA_1
        14.6%
        43.1
        49.7%
        96.8%
        0.1%
        NP_Day1_adherentcells_DMSO_1
        19.7%
        49.7
        51.2%
        95.7%
        0.0%
        NP_Day1_adherentcells_DMSO_2
        20.1%
        48.1
        54.6%
        96.2%
        0.0%
        NP_Day1_adherentcells_DMSO_3
        27.6%
        52.7
        53.4%
        94.9%
        0.1%
        NP_Day1_adherentcells_TA_1
        13.7%
        48.5
        49.9%
        96.5%
        0.0%
        NP_Day1_adherentcells_TA_2
        21.4%
        52.4
        54.9%
        97.5%
        0.0%
        NP_Day1_adherentcells_TA_3
        17.3%
        52.7
        49.6%
        96.5%
        0.0%

        Workflow explanation

        Preprocessing of reads was done automatically by seq2science v1.2.0 using the alignment workflow. Paired-end reads were trimmed with fastp v0.23.2 with default options. Genome assembly GRCh38.p13 was downloaded with genomepy 0.16.1. Reads were aligned with STAR v2.7.10b with default options. Afterwards, duplicate reads were marked with Picard MarkDuplicates v3.0.0. General alignment statistics were collected by samtools stats v1.16. 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'. The UCSC genome browser was used to visualize and inspect alignment. Quality control metrics were aggregated by MultiQC v1.14.

        Assembly stats

        Genome assembly GRCh38.p13 contains of 194 contigs, with a GC-content of 40.86%, and 4.96% consists of the letter N. The N50-L50 stats are 145138636-9 and the N75-L75 stats are 114364328-14. The genome annotation contains 39397 genes.

        fastp

        fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).DOI: 10.1093/bioinformatics/bty560.

        Filtered Reads

        Filtering statistics 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.

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        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
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        SamTools pre-sieve

        Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.

        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).

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        Alignment metrics

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

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        deepTools

        deepTools is a suite of tools to process and analyze deep sequencing data.DOI: 10.1093/nar/gkw257.

        PCA plot

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

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        Fingerprint plot

        Signal fingerprint according to plotFingerprint

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        Strandedness

        Strandedness package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.DOI: 10.1093/bioinformatics/bts356.

        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).

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        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 technical_replicates descriptivate_name
        HSCD12_DMSO_1bio GRCh38.p13 D12_supernatant_DMSO_1 D12_supernatant_DMSO_1
        HSCD12_DMSO_2bio GRCh38.p13 D12_supernatant_DMSO_2 D12_supernatant_DMSO_2
        HSCD12_DMSO_3bio GRCh38.p13 D12_supernatant_DMSO_3 D12_supernatant_DMSO_3
        HSCD12_RU1uM_1bio GRCh38.p13 D12_supernatant_RU1uM_1 D12_supernatant_RU1uM_1
        HSCD12_RU1uM_2bio GRCh38.p13 D12_supernatant_RU1uM_2 D12_supernatant_RU1uM_2
        HSCD12_RU1uM_3bio GRCh38.p13 D12_supernatant_RU1uM_3 D12_supernatant_RU1uM_3
        HSCD12_RU1uMTA100nM_1bio GRCh38.p13 D12_supernatant_RU1uMTA100nM_1 D12_supernatant_RU1uMTA100nM_1
        HSCD12_RU1uMTA100nM_2bio GRCh38.p13 D12_supernatant_RU1uMTA100nM_2 D12_supernatant_RU1uMTA100nM_2
        HSCD12_RU1uMTA100nM_3bio GRCh38.p13 D12_supernatant_RU1uMTA100nM_3 D12_supernatant_RU1uMTA100nM_3
        HSCD12_RU1uMTA1uM_1bio GRCh38.p13 D12_supernatant_RU1uMTA1uM_1 D12_supernatant_RU1uMTA1uM_1
        HSCD12_RU1uMTA1uM_2bio GRCh38.p13 D12_supernatant_RU1uMTA1uM_2 D12_supernatant_RU1uMTA1uM_2
        HSCD12_RU1uMTA1uM_3bio GRCh38.p13 D12_supernatant_RU1uMTA1uM_3 D12_supernatant_RU1uMTA1uM_3
        HSCD12_TA100nM_1bio GRCh38.p13 D12_supernatant_TA100nM_1 D12_supernatant_TA100nM_1
        HSCD12_TA100nM_2bio GRCh38.p13 D12_supernatant_TA100nM_2 D12_supernatant_TA100nM_2
        HSCD12_TA100nM_3bio GRCh38.p13 D12_supernatant_TA100nM_3 D12_supernatant_TA100nM_3
        HSCD12_TA1uM_1bio GRCh38.p13 D12_supernatant_TA1uM_1 D12_supernatant_TA1uM_1
        HSCD12_TA1uM_2bio GRCh38.p13 D12_supernatant_TA1uM_2 D12_supernatant_TA1uM_2
        HSCD12_TA1uM_3bio GRCh38.p13 D12_supernatant_TA1uM_3 D12_supernatant_TA1uM_3
        NP_Day10_supernatant_DMSO_1 GRCh38.p13 D10_supernatant_DMSO_1 D10_supernatant_DMSO_1
        NP_Day10_supernatant_DMSO_2 GRCh38.p13 D10_supernatant_DMSO_2 D10_supernatant_DMSO_2
        NP_Day10_supernatant_DMSO_3 GRCh38.p13 D10_supernatant_DMSO_3 D10_supernatant_DMSO_3
        NP_Day10_supernatant_TA_1 GRCh38.p13 D10_supernatant_TA_1 D10_supernatant_TA_1
        NP_Day10_supernatant_TA_2 GRCh38.p13 D10_supernatant_TA_2 D10_supernatant_TA_2
        NP_Day10_supernatant_TA_3 GRCh38.p13 D10_supernatant_TA_3 D10_supernatant_TA_3
        NP_Day12_adherent_DMSO_1 GRCh38.p13 D12_adherent_DMSO_1 D12_adherent_DMSO_1
        NP_Day12_adherent_DMSO_2 GRCh38.p13 D12_adherent_DMSO_2 D12_adherent_DMSO_2
        NP_Day12_adherent_DMSO_3 GRCh38.p13 D12_adherent_DMSO_3 D12_adherent_DMSO_3
        NP_Day12_adherent_TA_1 GRCh38.p13 D12_adherent_TA_1 D12_adherent_TA_1
        NP_Day12_adherent_TA_2 GRCh38.p13 D12_adherent_TA_2 D12_adherent_TA_2
        NP_Day12_adherent_TA_3 GRCh38.p13 D12_adherent_TA_3 D12_adherent_TA_3
        NP_Day12_supernatant_DMSO_1 GRCh38.p13 D12_supernatant_DMSO_1 D12_supernatant_DMSO_1
        NP_Day12_supernatant_DMSO_2 GRCh38.p13 D12_supernatant_DMSO_2 D12_supernatant_DMSO_2
        NP_Day12_supernatant_DMSO_3 GRCh38.p13 D12_supernatant_DMSO_3 D12_supernatant_DMSO_3
        NP_Day12_supernatant_TA_1 GRCh38.p13 D12_supernatant_TA_1 D12_supernatant_TA_1
        NP_Day12_supernatant_TA_2 GRCh38.p13 D12_supernatant_TA_2 D12_supernatant_TA_2
        NP_Day12_supernatant_TA_3 GRCh38.p13 D12_supernatant_TA_3 D12_supernatant_TA_3
        NP_Day18_adherent_DMSO_2 GRCh38.p13 D18_adherent_DMSO_2 D18_adherent_DMSO_2
        NP_Day18_adherent_DMSO_3 GRCh38.p13 D18_adherent_DMSO_3 D18_adherent_DMSO_3
        NP_Day18_adherent_TA_2 GRCh38.p13 D18_adherent_TA_2 D18_adherent_TA_2
        NP_Day18_adherent_TA_3 GRCh38.p13 D18_adherent_TA_3 D18_adherent_TA_3
        NP_Day18_supernatant_DMSO_2 GRCh38.p13 D18_supernatant_DMSO_2 D18_supernatant_DMSO_2
        NP_Day18_supernatant_DMSO_3 GRCh38.p13 D18_supernatant_DMSO_3 D18_supernatant_DMSO_3
        NP_Day18_supernatant_TA_2 GRCh38.p13 D18_supernatant_TA_2 D18_supernatant_TA_2
        NP_Day18_supernatant_TA_3 GRCh38.p13 D18_supernatant_TA_3 D18_supernatant_TA_3
        NP_Day19_adherent_DMSO_1 GRCh38.p13 D19_adherent_DMSO_1 D19_adherent_DMSO_1
        NP_Day19_adherent_TA_1 GRCh38.p13 D19_adherent_TA_1 D19_adherent_TA_1
        NP_Day19_supernatant_DMSO_1 GRCh38.p13 D19_supernatant_DMSO_1 D19_supernatant_DMSO_1
        NP_Day19_supernatant_TA_1 GRCh38.p13 D19_supernatant_TA_1 D19_supernatant_TA_1
        NP_Day1_adherentcells_DMSO_1 GRCh38.p13 D1_adherent_TA_DMSO_1 D1_adherent_TA_DMSO_1
        NP_Day1_adherentcells_DMSO_2 GRCh38.p13 D1_adherent_TA_DMSO_2 D1_adherent_TA_DMSO_2
        NP_Day1_adherentcells_DMSO_3 GRCh38.p13 D1_adherent_TA_DMSO_3 D1_adherent_TA_DMSO_3
        NP_Day1_adherentcells_TA_1 GRCh38.p13 D1_adherent_TA_1 D1_adherent_TA_1
        NP_Day1_adherentcells_TA_2 GRCh38.p13 D1_adherent_TA_2 D1_adherent_TA_2
        NP_Day1_adherentcells_TA_3 GRCh38.p13 D1_adherent_TA_3 D1_adherent_TA_3

        The config file used for this run: 
        # tab-separated file of the samples
samples: /home/slrinzema/ceph/ghe//samples/samples_no_replicates.tsv

# pipeline file locations
result_dir: ./results_no_replicates  # where to store results
genome_dir: /ceph/rimlsfnwi/data/genomes/  # where to look for or download the genomes
fastq_dir: /home/slrinzema/ceph/ghe/samples  # where to look for or download the fastqs


# contact info for multiqc report and trackhub
email: slrinzema@science.ru.nl

# produce a UCSC trackhub?
create_trackhub: true

# how to handle replicates
technical_replicates: merge

# which trimmer to use
trimmer: fastp

# which quantifier to use
quantifier: salmon

# 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_primary_align: true
remove_dups: false

        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

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