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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 (d129b7d)

        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 v0.5.6, 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
        rna-seq
        Date
        November 01, 2021
        Project
        xt_rna
        Contact E-mail
        none@provided.com

        Report generated on 2021-11-03, 03:20 based on data in:

        Change sample names:

        General Statistics

        Showing 127/127 rows and 11/21 columns.
        Sample Name% DuplicationGC content% PF% AdapterInsert Size% Dups% MappedM Total seqsGenome coverageM Genome readsM MT genome reads
        GSM1606183
        2.3%
        44.5%
        92.3%
        1.0%
        161 bp
        9.6%
        100.0%
        72.9
        3.9 X
        74.9
        0.7
        GSM1606184
        1.4%
        44.4%
        97.1%
        0.8%
        162 bp
        7.9%
        100.0%
        74.6
        4.0 X
        76.8
        0.6
        GSM1606185
        1.5%
        44.5%
        97.0%
        1.0%
        159 bp
        6.0%
        100.0%
        37.6
        2.1 X
        39.1
        0.3
        GSM1606186
        2.8%
        44.4%
        97.1%
        1.1%
        157 bp
        11.3%
        100.0%
        88.5
        4.9 X
        92.7
        0.9
        GSM1606187
        2.6%
        44.6%
        97.3%
        1.1%
        159 bp
        11.3%
        100.0%
        84.4
        4.7 X
        88.7
        0.9
        GSM1606188
        2.1%
        44.7%
        97.5%
        1.0%
        162 bp
        9.4%
        100.0%
        56.8
        3.1 X
        59.7
        0.6
        GSM1606189
        2.5%
        44.8%
        84.9%
        0.8%
        164 bp
        11.7%
        100.0%
        66.1
        3.7 X
        69.8
        0.9
        GSM1606190
        2.5%
        44.8%
        96.5%
        1.0%
        164 bp
        12.0%
        100.0%
        61.0
        3.4 X
        64.5
        0.8
        GSM1606191
        2.0%
        45.0%
        97.1%
        1.0%
        166 bp
        10.1%
        100.0%
        42.6
        2.4 X
        44.9
        0.7
        GSM1606192
        1.3%
        45.1%
        97.4%
        1.1%
        167 bp
        10.0%
        100.0%
        49.6
        2.8 X
        52.5
        0.9
        GSM1606193
        2.7%
        44.9%
        97.2%
        1.0%
        166 bp
        15.0%
        100.0%
        67.7
        3.8 X
        72.0
        1.1
        GSM1606194
        2.1%
        44.9%
        97.3%
        1.1%
        164 bp
        12.4%
        100.0%
        42.9
        2.4 X
        45.7
        0.8
        GSM1606195
        2.0%
        45.0%
        87.3%
        0.9%
        166 bp
        12.0%
        100.0%
        39.5
        2.2 X
        42.3
        0.5
        GSM1606196
        2.7%
        44.8%
        96.9%
        1.1%
        162 bp
        16.5%
        100.0%
        66.5
        3.7 X
        71.0
        1.3
        GSM1606197
        3.1%
        44.9%
        97.1%
        1.1%
        164 bp
        18.0%
        100.0%
        78.0
        4.4 X
        83.5
        1.4
        GSM1606198
        2.8%
        45.0%
        97.1%
        1.1%
        170 bp
        16.8%
        100.0%
        76.8
        4.3 X
        82.3
        1.0
        GSM1606199
        2.3%
        44.8%
        97.1%
        1.5%
        150 bp
        14.6%
        100.0%
        47.8
        2.7 X
        51.0
        1.0
        GSM1606200
        2.1%
        44.9%
        97.1%
        0.7%
        163 bp
        14.4%
        100.0%
        60.0
        3.4 X
        64.3
        1.1
        GSM1606201
        2.2%
        45.0%
        92.1%
        0.7%
        163 bp
        16.8%
        100.0%
        81.3
        4.6 X
        86.7
        1.6
        GSM1606202
        2.6%
        44.9%
        96.8%
        0.8%
        160 bp
        16.1%
        100.0%
        70.7
        4.0 X
        75.7
        1.4
        GSM1606203
        1.9%
        44.8%
        97.2%
        0.8%
        161 bp
        14.7%
        100.0%
        71.3
        4.0 X
        76.3
        1.3
        GSM1606204
        1.9%
        44.8%
        97.3%
        0.7%
        162 bp
        14.5%
        100.0%
        67.6
        3.8 X
        72.3
        1.3
        GSM1606205
        2.1%
        44.8%
        97.2%
        0.7%
        165 bp
        14.9%
        100.0%
        78.8
        4.4 X
        84.4
        1.4
        GSM1606206
        2.1%
        44.8%
        97.3%
        0.7%
        161 bp
        15.3%
        100.0%
        82.4
        4.6 X
        88.1
        1.5
        GSM1606207
        1.7%
        45.0%
        94.6%
        0.7%
        166 bp
        13.0%
        100.0%
        70.9
        4.0 X
        76.6
        0.9
        GSM1606208
        1.9%
        44.9%
        97.1%
        0.8%
        159 bp
        12.3%
        100.0%
        52.2
        3.0 X
        56.3
        0.6
        GSM1606209
        2.2%
        44.9%
        97.3%
        0.9%
        157 bp
        14.3%
        100.0%
        67.9
        3.8 X
        72.8
        1.1
        GSM1606210
        2.1%
        44.9%
        97.3%
        0.9%
        158 bp
        13.5%
        100.0%
        60.8
        3.4 X
        65.3
        0.9
        GSM1606211
        2.1%
        44.9%
        97.3%
        0.9%
        157 bp
        14.0%
        100.0%
        64.2
        3.6 X
        68.5
        1.2
        GSM1606212
        2.3%
        44.9%
        97.4%
        0.9%
        157 bp
        15.3%
        100.0%
        80.0
        4.5 X
        85.5
        1.5
        GSM1606213
        2.0%
        44.8%
        95.0%
        0.8%
        158 bp
        13.2%
        100.0%
        60.8
        3.4 X
        64.9
        1.0
        GSM1606214
        1.9%
        44.8%
        97.2%
        0.8%
        159 bp
        12.7%
        100.0%
        57.7
        3.2 X
        61.6
        0.9
        GSM1606215
        1.9%
        44.9%
        97.5%
        0.8%
        159 bp
        13.2%
        100.0%
        63.9
        3.6 X
        68.0
        1.1
        GSM1606216
        2.2%
        45.0%
        97.2%
        0.8%
        159 bp
        14.7%
        100.0%
        77.5
        4.3 X
        82.5
        1.3
        GSM1606217
        1.8%
        44.7%
        96.5%
        0.8%
        156 bp
        13.1%
        100.0%
        68.9
        3.9 X
        73.7
        0.8
        GSM1606218
        2.1%
        44.8%
        96.7%
        0.8%
        157 bp
        14.9%
        100.0%
        81.1
        4.6 X
        87.0
        0.7
        GSM1606219
        1.6%
        44.6%
        93.5%
        0.7%
        165 bp
        14.7%
        100.0%
        93.0
        5.2 X
        98.3
        1.8
        GSM1606220
        1.6%
        44.6%
        96.1%
        0.7%
        164 bp
        13.3%
        100.0%
        77.1
        4.3 X
        82.0
        1.3
        GSM1606221
        1.6%
        44.7%
        96.6%
        0.7%
        162 bp
        13.1%
        100.0%
        67.9
        3.8 X
        71.7
        1.4
        GSM1606222
        1.8%
        44.5%
        96.6%
        0.7%
        160 bp
        13.8%
        100.0%
        73.0
        4.1 X
        77.5
        1.1
        GSM1606223
        2.1%
        44.8%
        96.0%
        0.6%
        176 bp
        14.2%
        100.0%
        54.4
        3.0 X
        57.0
        1.1
        GSM1606224
        2.3%
        44.8%
        96.6%
        3.5%
        152 bp
        16.1%
        100.0%
        71.2
        3.9 X
        74.2
        1.8
        GSM1606225
        2.4%
        44.6%
        96.7%
        3.4%
        150 bp
        16.6%
        100.0%
        80.4
        4.4 X
        84.4
        1.9
        GSM1606226
        2.2%
        44.6%
        96.5%
        3.3%
        151 bp
        15.4%
        100.0%
        65.9
        3.6 X
        69.0
        1.7
        GSM1606227
        2.0%
        45.0%
        96.4%
        3.1%
        155 bp
        14.1%
        100.0%
        48.3
        2.6 X
        50.2
        1.2
        GSM1606228
        2.4%
        44.8%
        96.5%
        3.1%
        152 bp
        16.3%
        100.0%
        75.0
        4.1 X
        78.2
        1.9
        GSM1606229
        1.9%
        45.6%
        96.6%
        2.8%
        163 bp
        15.6%
        100.0%
        45.8
        2.5 X
        47.5
        1.3
        GSM1606230
        1.6%
        45.2%
        96.9%
        2.8%
        158 bp
        12.1%
        100.0%
        33.7
        1.8 X
        35.1
        0.9
        GSM1606231
        2.1%
        45.0%
        97.0%
        2.7%
        161 bp
        16.6%
        100.0%
        67.4
        3.7 X
        69.9
        2.0
        GSM1606232
        2.2%
        45.8%
        96.8%
        3.7%
        167 bp
        17.4%
        100.0%
        56.3
        3.1 X
        58.8
        1.5
        GSM1606233
        2.5%
        45.4%
        96.7%
        2.8%
        162 bp
        19.5%
        100.0%
        73.8
        4.0 X
        76.3
        2.8
        GSM1606234
        1.8%
        44.7%
        97.0%
        3.3%
        153 bp
        14.6%
        100.0%
        55.2
        3.0 X
        57.1
        2.0
        GSM1606235
        2.1%
        44.9%
        97.0%
        2.7%
        161 bp
        17.0%
        100.0%
        78.9
        4.3 X
        81.5
        2.8
        GSM1606265
        3.9%
        45.0%
        72.1%
        0.5%
        182 bp
        14.8%
        100.0%
        37.5
        2.1 X
        40.3
        0.5
        GSM1606266
        2.3%
        45.0%
        72.2%
        0.5%
        200 bp
        9.7%
        100.0%
        27.8
        1.6 X
        29.9
        0.2
        GSM1606267
        2.9%
        46.0%
        72.3%
        0.5%
        189 bp
        18.5%
        100.0%
        52.8
        2.9 X
        54.9
        1.5
        GSM1606268
        3.5%
        46.2%
        71.8%
        0.6%
        191 bp
        19.7%
        100.0%
        51.5
        2.8 X
        53.8
        1.3
        GSM1606327
        1.6%
        44.6%
        93.2%
        0.5%
        166 bp
        11.6%
        100.0%
        63.0
        3.4 X
        64.9
        0.5
        GSM1606328
        1.3%
        44.3%
        92.7%
        0.5%
        165 bp
        9.0%
        100.0%
        43.6
        2.4 X
        45.1
        0.4
        GSM1606329
        1.7%
        44.4%
        93.3%
        0.6%
        162 bp
        12.2%
        100.0%
        74.7
        4.1 X
        77.6
        0.6
        GSM1606330
        1.3%
        44.6%
        93.4%
        0.6%
        161 bp
        10.5%
        100.0%
        56.9
        3.1 X
        59.5
        0.5
        GSM1606331
        1.3%
        44.4%
        92.4%
        0.5%
        163 bp
        10.0%
        100.0%
        49.6
        2.7 X
        52.1
        0.5
        GSM1606332
        1.9%
        44.3%
        92.1%
        0.6%
        163 bp
        13.2%
        100.0%
        63.2
        3.5 X
        66.7
        0.7
        GSM1606333
        1.4%
        44.6%
        92.4%
        0.7%
        159 bp
        11.9%
        100.0%
        50.1
        2.8 X
        52.6
        0.6
        GSM1606334
        1.6%
        44.5%
        91.6%
        0.6%
        163 bp
        14.2%
        100.0%
        58.1
        3.2 X
        61.0
        0.8
        GSM1606335
        1.2%
        44.6%
        92.2%
        0.5%
        166 bp
        12.9%
        100.0%
        47.0
        2.6 X
        49.4
        0.7
        GSM1606336
        1.4%
        44.6%
        92.5%
        0.5%
        171 bp
        15.7%
        100.0%
        55.9
        3.1 X
        58.8
        0.9
        GSM1606337
        1.5%
        44.7%
        90.6%
        0.5%
        167 bp
        16.3%
        100.0%
        54.4
        3.0 X
        57.3
        0.8
        GSM1606338
        1.3%
        44.7%
        90.5%
        0.6%
        166 bp
        15.2%
        100.0%
        46.2
        2.6 X
        48.7
        0.7
        GSM1606339
        1.5%
        44.8%
        90.8%
        0.6%
        163 bp
        16.8%
        100.0%
        45.9
        2.6 X
        48.6
        0.7
        GSM1606340
        1.7%
        44.9%
        89.8%
        0.6%
        162 bp
        18.7%
        100.0%
        57.6
        3.2 X
        61.2
        0.6
        GSM1606341
        1.7%
        44.8%
        90.6%
        0.6%
        162 bp
        18.7%
        100.0%
        65.4
        3.7 X
        69.5
        0.9
        GSM1606342
        1.2%
        44.7%
        90.9%
        0.5%
        161 bp
        15.7%
        100.0%
        49.1
        2.7 X
        52.2
        0.7
        GSM1606343
        2.0%
        44.9%
        92.1%
        0.6%
        167 bp
        18.5%
        100.0%
        62.8
        3.5 X
        66.4
        1.0
        GSM1606344
        2.1%
        44.9%
        92.1%
        0.6%
        164 bp
        20.3%
        100.0%
        73.7
        4.1 X
        77.9
        1.2
        GSM1606345
        1.6%
        45.0%
        92.1%
        0.6%
        165 bp
        16.0%
        100.0%
        50.2
        2.8 X
        53.5
        0.5
        GSM1606346
        4.3%
        45.5%
        97.5%
        0.8%
        169 bp
        19.5%
        100.0%
        67.7
        3.8 X
        71.9
        0.8
        GSM1606347
        1.7%
        44.8%
        92.1%
        0.6%
        165 bp
        17.0%
        100.0%
        59.8
        3.4 X
        63.6
        0.8
        GSM1606348
        1.5%
        44.8%
        92.5%
        0.6%
        163 bp
        15.0%
        100.0%
        48.9
        2.7 X
        52.0
        0.7
        GSM1606349
        1.6%
        44.6%
        89.8%
        0.6%
        161 bp
        16.1%
        100.0%
        53.5
        3.0 X
        56.7
        0.8
        GSM1606350
        1.8%
        44.8%
        89.5%
        0.6%
        161 bp
        20.5%
        100.0%
        97.9
        5.5 X
        103.7
        1.2
        GSM1606351
        0.9%
        44.5%
        90.3%
        0.5%
        159 bp
        11.2%
        100.0%
        34.5
        1.9 X
        36.8
        0.4
        GSM1606352
        1.0%
        44.8%
        88.8%
        0.5%
        165 bp
        13.0%
        100.0%
        37.8
        2.1 X
        40.1
        0.4
        GSM1606353
        1.1%
        44.5%
        89.6%
        0.6%
        161 bp
        12.8%
        100.0%
        41.7
        2.4 X
        44.7
        0.5
        GSM1606354
        1.2%
        45.0%
        89.9%
        0.6%
        162 bp
        14.4%
        100.0%
        47.4
        2.7 X
        50.4
        0.3
        GSM1606355
        1.7%
        45.0%
        91.0%
        0.6%
        165 bp
        15.7%
        100.0%
        55.0
        3.1 X
        58.4
        0.5
        GSM1606356
        1.7%
        44.8%
        90.9%
        0.6%
        164 bp
        16.1%
        100.0%
        61.4
        3.4 X
        65.1
        0.7
        GSM1606357
        1.4%
        44.8%
        91.3%
        0.5%
        163 bp
        14.7%
        100.0%
        47.6
        2.7 X
        50.4
        0.6
        GSM1606358
        1.4%
        44.9%
        90.3%
        0.5%
        163 bp
        15.6%
        100.0%
        56.6
        3.1 X
        59.7
        0.7
        GSM1606359
        1.6%
        44.8%
        90.9%
        0.5%
        164 bp
        16.8%
        100.0%
        71.4
        4.0 X
        75.4
        0.8
        GSM1606360
        1.3%
        45.0%
        91.2%
        0.6%
        165 bp
        13.3%
        100.0%
        45.8
        2.6 X
        48.5
        0.5
        GSM1606361
        1.8%
        44.8%
        95.0%
        0.6%
        171 bp
        16.5%
        100.0%
        50.0
        2.8 X
        53.1
        0.4
        GSM1606362
        1.8%
        45.0%
        94.8%
        0.6%
        169 bp
        15.1%
        100.0%
        61.7
        3.5 X
        65.5
        0.7
        GSM1606363
        1.4%
        44.7%
        94.7%
        0.6%
        170 bp
        13.0%
        100.0%
        56.1
        3.1 X
        59.5
        0.8
        GSM1606364
        2.5%
        44.7%
        94.4%
        0.5%
        189 bp
        22.8%
        100.0%
        58.1
        3.2 X
        61.2
        0.6
        GSM1606365
        1.7%
        45.4%
        94.8%
        0.5%
        172 bp
        15.8%
        100.0%
        58.4
        3.2 X
        61.3
        1.0
        GSM1606366
        1.6%
        45.1%
        95.1%
        0.6%
        169 bp
        14.8%
        100.0%
        56.4
        3.1 X
        59.2
        1.0
        GSM1606367
        2.2%
        45.5%
        94.2%
        0.6%
        177 bp
        18.2%
        100.0%
        65.8
        3.6 X
        69.0
        1.1
        GSM919922
        2.2%
        50.9%
        88.7%
        1.5%
        493 bp
        7.7%
        100.0%
        18.6
        1.4 X
        19.7
        0.2
        GSM919923
        3.0%
        50.1%
        88.4%
        1.3%
        540 bp
        9.6%
        100.0%
        15.9
        1.2 X
        17.0
        0.2
        GSM919924
        3.9%
        50.3%
        88.0%
        1.2%
        556 bp
        11.3%
        100.0%
        17.5
        1.3 X
        18.8
        0.2
        GSM919925
        6.0%
        49.9%
        88.7%
        0.9%
        556 bp
        18.7%
        100.0%
        20.1
        1.5 X
        21.4
        0.4
        GSM919926
        1.6%
        50.6%
        89.8%
        1.0%
        675 bp
        14.4%
        100.0%
        20.7
        1.6 X
        22.6
        0.3
        GSM919927
        3.8%
        49.8%
        89.3%
        1.0%
        649 bp
        15.5%
        100.0%
        18.0
        1.4 X
        19.5
        0.2
        GSM919928
        3.5%
        50.3%
        90.1%
        1.1%
        597 bp
        17.1%
        100.0%
        19.3
        1.5 X
        20.9
        0.3
        GSM919929
        1.5%
        50.7%
        90.3%
        1.2%
        671 bp
        14.7%
        100.0%
        21.8
        1.7 X
        23.8
        0.3
        GSM919930
        3.7%
        49.8%
        90.3%
        1.0%
        622 bp
        16.6%
        100.0%
        18.2
        1.3 X
        19.1
        0.6
        GSM919931
        3.5%
        50.1%
        90.2%
        1.0%
        588 bp
        17.9%
        100.0%
        20.7
        1.5 X
        21.9
        0.6
        GSM919932
        1.3%
        50.8%
        90.8%
        1.3%
        710 bp
        16.0%
        100.0%
        22.8
        1.7 X
        24.6
        0.4
        GSM919933
        1.3%
        50.7%
        91.0%
        1.2%
        766 bp
        15.7%
        100.0%
        21.2
        1.6 X
        22.7
        0.4
        GSM919934
        1.3%
        50.9%
        90.9%
        1.2%
        762 bp
        16.3%
        100.0%
        20.6
        1.5 X
        21.9
        0.5
        GSM919935
        1.3%
        50.7%
        91.4%
        1.1%
        785 bp
        17.2%
        100.0%
        23.5
        1.8 X
        25.2
        0.5
        GSM919943
        2.1%
        51.1%
        98.3%
        0.4%
        905 bp
        9.9%
        100.0%
        21.1
        1.5 X
        21.9
        0.2
        GSM919944
        2.1%
        50.8%
        98.3%
        0.5%
        804 bp
        9.6%
        100.0%
        20.5
        1.5 X
        21.6
        0.3
        GSM919945
        2.3%
        50.8%
        98.2%
        0.6%
        769 bp
        11.6%
        100.0%
        18.8
        1.4 X
        20.1
        0.3
        GSM919946
        2.3%
        50.9%
        98.2%
        0.6%
        742 bp
        14.6%
        100.0%
        19.2
        1.4 X
        20.6
        0.4
        GSM919947
        2.6%
        50.8%
        98.2%
        0.6%
        780 bp
        16.3%
        100.0%
        17.7
        1.3 X
        19.1
        0.3
        GSM919948
        2.4%
        50.8%
        98.2%
        0.5%
        754 bp
        16.9%
        100.0%
        17.3
        1.3 X
        18.8
        0.3
        GSM919949
        2.8%
        51.1%
        98.4%
        0.5%
        820 bp
        20.0%
        100.0%
        23.4
        1.8 X
        25.4
        0.3
        GSM919950
        3.3%
        50.5%
        98.8%
        0.5%
        767 bp
        19.5%
        100.0%
        16.3
        1.2 X
        17.6
        0.4
        GSM919951
        3.5%
        50.5%
        98.9%
        0.5%
        838 bp
        21.7%
        100.0%
        21.0
        1.5 X
        22.4
        0.6
        GSM919952
        3.3%
        50.4%
        98.8%
        0.5%
        822 bp
        22.1%
        100.0%
        18.6
        1.4 X
        19.6
        0.6
        GSM919953
        3.6%
        50.4%
        98.8%
        0.5%
        777 bp
        22.8%
        100.0%
        18.7
        1.4 X
        20.1
        0.5
        GSM919954
        3.3%
        50.5%
        98.9%
        0.5%
        814 bp
        21.8%
        100.0%
        20.5
        1.5 X
        22.1
        0.4
        GSM919955
        3.5%
        50.4%
        98.8%
        0.5%
        865 bp
        24.2%
        100.0%
        20.5
        1.5 X
        21.8
        0.7
        GSM919956
        3.0%
        51.2%
        98.9%
        0.5%
        872 bp
        23.0%
        100.0%
        21.1
        1.6 X
        22.9
        0.3
        GSM919957
        2.9%
        51.2%
        98.9%
        0.5%
        870 bp
        24.4%
        100.0%
        22.5
        1.7 X
        24.6
        0.4

        Workflow explanation

        Preprocessing of reads was done automatically with workflow tool seq2science v0.5.6. Public samples were downloaded from the Sequence Read Archive with help of the ncbi e-utilities and pysradb. Genome assembly Xenopus_tropicalis_v9.1 was downloaded with genomepy 0.10.0. Paired-end reads were trimmed with fastp v0.20.1 with default options. Reads were aligned with STAR v2.7.6a with default options. Decoy transcript were generated in order improve improve Salmon indexing accuracy using the scripts provided in the Salmon manual Afterwards, duplicate reads were marked with Picard MarkDuplicates v2.23.8. General alignment statistics were collected by samtools stats v1.11. Mapped reads were removed if they did not have a minimum mapping quality of 255, were a (secondary) multimapper or aligned inside the ENCODE blacklist. Transcript abundances were quantified with Salmon v1.5.2 with options '--seqBias --gcBias --validateMappings --recoverOrphans'. Transcript abundance estimations were aggregated and converted to gene counts using tximeta v1.10.0. Sample sequencing strandedness was inferred using RSeQC v4.0.0 in order to improve quantification accuracy. Deeptools v3.5.0 was used for the fingerprint, profile, correlation and dendrogram/heatmap plots, where the heatmap was made with options '--distanceBetweenBins 9000 --binSize 1000'. RNA-seq read duplication types were analyzed using dupRadar v1.20.0. The UCSC genome browser was used to visualize and inspect alignment. Quality control metrics were aggregated by MultiQC v1.11.

        fastp

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

        Filtered Reads

        Filtering statistics of sampled reads.

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

        Duplication Rates

        Duplication rates of sampled reads.

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

        Insert Sizes

        Insert size estimation of sampled reads.

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

        Sequence Quality

        Average sequencing quality over each base of all reads.

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

        GC Content

        Average GC content over each base of all reads.

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

        N content

        Average N content over each base of all reads.

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

        Picard

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

        Insert Size

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

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

        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

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

        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).

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

        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

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

        Strandedness

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

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

        Infer experiment

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

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

        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 source mpf hpf stage descriptive_name
        GSM1606183 Xenopus_tropicalis_v9.1 owens_a1 240 4 stage8 owens_a1_240
        GSM1606184 Xenopus_tropicalis_v9.1 owens_a1 270 4.5 stage9 owens_a1_270
        GSM1606185 Xenopus_tropicalis_v9.1 owens_a1 300 5 stage9 owens_a1_300
        GSM1606186 Xenopus_tropicalis_v9.1 owens_a1 330 5.5 stage9 owens_a1_330
        GSM1606187 Xenopus_tropicalis_v9.1 owens_a1 360 6 stage9 owens_a1_360
        GSM1606188 Xenopus_tropicalis_v9.1 owens_a1 390 6.5 stage10 owens_a1_390
        GSM1606189 Xenopus_tropicalis_v9.1 owens_a1 420 7 stage10 owens_a1_420
        GSM1606190 Xenopus_tropicalis_v9.1 owens_a1 450 7.5 stage10 owens_a1_450
        GSM1606191 Xenopus_tropicalis_v9.1 owens_a1 480 8 stage11 owens_a1_480
        GSM1606192 Xenopus_tropicalis_v9.1 owens_a1 510 8.5 stage12 owens_a1_510
        GSM1606193 Xenopus_tropicalis_v9.1 owens_a1 540 9 stage12 owens_a1_540
        GSM1606194 Xenopus_tropicalis_v9.1 owens_a1 570 9.5 stage12 owens_a1_570
        GSM1606195 Xenopus_tropicalis_v9.1 owens_a1 600 10 stage12 owens_a1_600
        GSM1606196 Xenopus_tropicalis_v9.1 owens_a1 630 10.5 stage12.5 owens_a1_630
        GSM1606197 Xenopus_tropicalis_v9.1 owens_a1 660 11 stage12.5 owens_a1_660
        GSM1606198 Xenopus_tropicalis_v9.1 owens_a1 690 11.5 stage12.5 owens_a1_690
        GSM1606199 Xenopus_tropicalis_v9.1 owens_a1 720 12 stage13 owens_a1_720
        GSM1606200 Xenopus_tropicalis_v9.1 owens_a1 750 12.5 stage13 owens_a1_750
        GSM1606201 Xenopus_tropicalis_v9.1 owens_a1 780 13 stage13 owens_a1_780
        GSM1606202 Xenopus_tropicalis_v9.1 owens_a1 810 13.5 stage14 owens_a1_810
        GSM1606203 Xenopus_tropicalis_v9.1 owens_a1 840 14 stage14 owens_a1_840
        GSM1606204 Xenopus_tropicalis_v9.1 owens_a1 870 14.5 stage15 owens_a1_870
        GSM1606205 Xenopus_tropicalis_v9.1 owens_a1 900 15 stage17 owens_a1_900
        GSM1606206 Xenopus_tropicalis_v9.1 owens_a1 930 15.5 stage19 owens_a1_930
        GSM1606207 Xenopus_tropicalis_v9.1 owens_a1 960 16 stage20 owens_a1_960
        GSM1606208 Xenopus_tropicalis_v9.1 owens_a1 990 16.5 stage21 owens_a1_990
        GSM1606209 Xenopus_tropicalis_v9.1 owens_a1 1020 17 stage21 owens_a1_1020
        GSM1606210 Xenopus_tropicalis_v9.1 owens_a1 1050 17.5 stage22 owens_a1_1050
        GSM1606211 Xenopus_tropicalis_v9.1 owens_a1 1080 18 stage22 owens_a1_1080
        GSM1606212 Xenopus_tropicalis_v9.1 owens_a1 1110 18.5 stage23 owens_a1_1110
        GSM1606213 Xenopus_tropicalis_v9.1 owens_a1 1140 19 stage24 owens_a1_1140
        GSM1606214 Xenopus_tropicalis_v9.1 owens_a1 1170 19.5 stage24 owens_a1_1170
        GSM1606215 Xenopus_tropicalis_v9.1 owens_a1 1200 20 stage24 owens_a1_1200
        GSM1606216 Xenopus_tropicalis_v9.1 owens_a1 1230 20.5 stage24 owens_a1_1230
        GSM1606217 Xenopus_tropicalis_v9.1 owens_a1 1260 21 stage25 owens_a1_1260
        GSM1606218 Xenopus_tropicalis_v9.1 owens_a1 1290 21.5 stage25 owens_a1_1290
        GSM1606219 Xenopus_tropicalis_v9.1 owens_a1 1320 22 stage25 owens_a1_1320
        GSM1606220 Xenopus_tropicalis_v9.1 owens_a1 1350 22.5 stage26 owens_a1_1350
        GSM1606221 Xenopus_tropicalis_v9.1 owens_a1 1380 23 stage26 owens_a1_1380
        GSM1606222 Xenopus_tropicalis_v9.1 owens_a1 1410 23.5 stage26 owens_a1_1410
        GSM1606223 Xenopus_tropicalis_v9.1 owens_a1 1440 24 stage27 owens_a1_1440
        GSM1606224 Xenopus_tropicalis_v9.1 owens_a1 1500 25 stage27 owens_a1_1500
        GSM1606225 Xenopus_tropicalis_v9.1 owens_a1 1560 26 stage27 owens_a1_1560
        GSM1606226 Xenopus_tropicalis_v9.1 owens_a1 1620 27 stage28 owens_a1_1620
        GSM1606227 Xenopus_tropicalis_v9.1 owens_a1 1680 28 stage28 owens_a1_1680
        GSM1606228 Xenopus_tropicalis_v9.1 owens_a1 1740 29 stage30 owens_a1_1740
        GSM1606229 Xenopus_tropicalis_v9.1 owens_a1 1800 30 stage31 owens_a1_1800
        GSM1606230 Xenopus_tropicalis_v9.1 owens_a1 1860 31 stage32 owens_a1_1860
        GSM1606231 Xenopus_tropicalis_v9.1 owens_a1 1920 32 stage32 owens_a1_1920
        GSM1606232 Xenopus_tropicalis_v9.1 owens_a1 1980 33 stage34 owens_a1_1980
        GSM1606233 Xenopus_tropicalis_v9.1 owens_a1 2040 34 stage34 owens_a1_2040
        GSM1606234 Xenopus_tropicalis_v9.1 owens_a1 2100 35 stage34 owens_a1_2100
        GSM1606235 Xenopus_tropicalis_v9.1 owens_a1 2160 36 stage35 owens_a1_2160
        GSM1606265 Xenopus_tropicalis_v9.1 owens_a2 690 11.5 stage12.5 owens_a2_690
        GSM1606266 Xenopus_tropicalis_v9.1 owens_a2 1290 21.5 stage25 owens_a2_1290
        GSM1606267 Xenopus_tropicalis_v9.1 owens_a2 1800 30 stage31 owens_a2_1800
        GSM1606268 Xenopus_tropicalis_v9.1 owens_a2 1980 33 stage34 owens_a2_1980
        GSM1606327 Xenopus_tropicalis_v9.1 owens_b1 240 4 stage8 owens_b1_240
        GSM1606328 Xenopus_tropicalis_v9.1 owens_b1 270 4.5 stage9 owens_b1_270
        GSM1606329 Xenopus_tropicalis_v9.1 owens_b1 300 5 stage9 owens_b1_300
        GSM1606330 Xenopus_tropicalis_v9.1 owens_b1 330 5.5 stage9 owens_b1_330
        GSM1606331 Xenopus_tropicalis_v9.1 owens_b1 360 6 stage9 owens_b1_360
        GSM1606332 Xenopus_tropicalis_v9.1 owens_b1 390 6.5 stage10 owens_b1_390
        GSM1606333 Xenopus_tropicalis_v9.1 owens_b1 420 7 stage10 owens_b1_420
        GSM1606334 Xenopus_tropicalis_v9.1 owens_b1 450 7.5 stage10 owens_b1_450
        GSM1606335 Xenopus_tropicalis_v9.1 owens_b1 480 8 stage11 owens_b1_480
        GSM1606336 Xenopus_tropicalis_v9.1 owens_b1 510 8.5 stage12 owens_b1_510
        GSM1606337 Xenopus_tropicalis_v9.1 owens_b1 540 9 stage12 owens_b1_540
        GSM1606338 Xenopus_tropicalis_v9.1 owens_b1 570 9.5 stage12 owens_b1_570
        GSM1606339 Xenopus_tropicalis_v9.1 owens_b1 600 10 stage12 owens_b1_600
        GSM1606340 Xenopus_tropicalis_v9.1 owens_b1 630 10.5 stage12.5 owens_b1_630
        GSM1606341 Xenopus_tropicalis_v9.1 owens_b1 660 11 stage12.5 owens_b1_660
        GSM1606342 Xenopus_tropicalis_v9.1 owens_b1 690 11.5 stage12.5 owens_b1_690
        GSM1606343 Xenopus_tropicalis_v9.1 owens_b1 720 12 stage13 owens_b1_720
        GSM1606344 Xenopus_tropicalis_v9.1 owens_b1 750 12.5 stage13 owens_b1_750
        GSM1606345 Xenopus_tropicalis_v9.1 owens_b1 780 13 stage13 owens_b1_780
        GSM1606346 Xenopus_tropicalis_v9.1 owens_b1 810 13.5 stage14 owens_b1_810
        GSM1606347 Xenopus_tropicalis_v9.1 owens_b1 840 14 stage14 owens_b1_840
        GSM1606348 Xenopus_tropicalis_v9.1 owens_b1 870 14.5 stage15 owens_b1_870
        GSM1606349 Xenopus_tropicalis_v9.1 owens_b1 900 15 stage17 owens_b1_900
        GSM1606350 Xenopus_tropicalis_v9.1 owens_b1 930 15.5 stage19 owens_b1_930
        GSM1606351 Xenopus_tropicalis_v9.1 owens_b1 960 16 stage20 owens_b1_960
        GSM1606352 Xenopus_tropicalis_v9.1 owens_b1 990 16.5 stage21 owens_b1_990
        GSM1606353 Xenopus_tropicalis_v9.1 owens_b1 1020 17 stage21 owens_b1_1020
        GSM1606354 Xenopus_tropicalis_v9.1 owens_b1 1050 17.5 stage22 owens_b1_1050
        GSM1606355 Xenopus_tropicalis_v9.1 owens_b1 1080 18 stage22 owens_b1_1080
        GSM1606356 Xenopus_tropicalis_v9.1 owens_b1 1110 18.5 stage23 owens_b1_1110
        GSM1606357 Xenopus_tropicalis_v9.1 owens_b1 1140 19 stage24 owens_b1_1140
        GSM1606358 Xenopus_tropicalis_v9.1 owens_b1 1170 19.5 stage24 owens_b1_1170
        GSM1606359 Xenopus_tropicalis_v9.1 owens_b1 1200 20 stage24 owens_b1_1200
        GSM1606360 Xenopus_tropicalis_v9.1 owens_b1 1230 20.5 stage24 owens_b1_1230
        GSM1606361 Xenopus_tropicalis_v9.1 owens_b1 1260 21 stage25 owens_b1_1260
        GSM1606362 Xenopus_tropicalis_v9.1 owens_b1 1290 21.5 stage25 owens_b1_1290
        GSM1606363 Xenopus_tropicalis_v9.1 owens_b1 1320 22 stage25 owens_b1_1320
        GSM1606364 Xenopus_tropicalis_v9.1 owens_b1 1350 22.5 stage26 owens_b1_1350
        GSM1606365 Xenopus_tropicalis_v9.1 owens_b1 1380 23 stage26 owens_b1_1380
        GSM1606366 Xenopus_tropicalis_v9.1 owens_b1 1410 23.5 stage26 owens_b1_1410
        GSM1606367 Xenopus_tropicalis_v9.1 owens_b1 1440 24 stage27 owens_b1_1440
        GSM919922 Xenopus_tropicalis_v9.1 tan_a 300 5 stage9 tan_a_300
        GSM919923 Xenopus_tropicalis_v9.1 tan_a 390 6.5 stage10 tan_a_390
        GSM919924 Xenopus_tropicalis_v9.1 tan_a 480 8 stage11 tan_a_480_rep1
        GSM919925 Xenopus_tropicalis_v9.1 tan_a 480 8 stage11 tan_a_480_rep2
        GSM919926 Xenopus_tropicalis_v9.1 tan_a 870 14.5 stage15 tan_a_870
        GSM919927 Xenopus_tropicalis_v9.1 tan_a 900 15 stage16 tan_a_900
        GSM919928 Xenopus_tropicalis_v9.1 tan_a 930 15.5 stage19 tan_a_930_rep1
        GSM919929 Xenopus_tropicalis_v9.1 tan_a 930 15.5 stage19 tan_a_930_rep2
        GSM919930 Xenopus_tropicalis_v9.1 tan_a 960 16 stage20 tan_a_960
        GSM919931 Xenopus_tropicalis_v9.1 tan_a 1050 17.5 stage22 tan_a_1050
        GSM919932 Xenopus_tropicalis_v9.1 tan_a 1140 19 stage24 tan_a_1140
        GSM919933 Xenopus_tropicalis_v9.1 tan_a 1620 27 stage28 tan_a_1620
        GSM919934 Xenopus_tropicalis_v9.1 tan_a 1800 30 stage31 tan_a_1800
        GSM919935 Xenopus_tropicalis_v9.1 tan_a 1980 33 stage33 tan_a_1980
        GSM919943 Xenopus_tropicalis_v9.1 tan_b 240 4 stage8 tan_b_240
        GSM919944 Xenopus_tropicalis_v9.1 tan_b 300 5 stage9 tan_b_300
        GSM919945 Xenopus_tropicalis_v9.1 tan_b 390 6.5 stage10 tan_b_390
        GSM919946 Xenopus_tropicalis_v9.1 tan_b 480 8 stage11 tan_b_480
        GSM919947 Xenopus_tropicalis_v9.1 tan_b 720 12 stage13 tan_b_720_rep1
        GSM919948 Xenopus_tropicalis_v9.1 tan_b 720 12 stage13 tan_b_720_rep2
        GSM919949 Xenopus_tropicalis_v9.1 tan_b 900 15 stage16 tan_b_900
        GSM919950 Xenopus_tropicalis_v9.1 tan_b 930 15.5 stage19 tan_b_930
        GSM919951 Xenopus_tropicalis_v9.1 tan_b 960 16 stage20 tan_b_960
        GSM919952 Xenopus_tropicalis_v9.1 tan_b 1050 17.5 stage22 tan_b_1050
        GSM919953 Xenopus_tropicalis_v9.1 tan_b 1140 19 stage24 tan_b_1140_rep1
        GSM919954 Xenopus_tropicalis_v9.1 tan_b 1140 19 stage24 tan_b_1140_rep2
        GSM919955 Xenopus_tropicalis_v9.1 tan_b 1620 27 stage28 tan_b_1620
        GSM919956 Xenopus_tropicalis_v9.1 tan_b 1800 30 stage31 tan_b_1800
        GSM919957 Xenopus_tropicalis_v9.1 tan_b 1980 33 stage33 tan_b_1980

        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: ../fastq/xenopus  # 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
create_qc_report: true

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

# which trimmer to use
trimmer: fastp

# which quantifier to use
quantifier: #htseq  # or salmon or featurecounts
  salmon:
    decoy_aware_index: true

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

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

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

        MultiQC v1.11 (d129b7d) - Written by Phil Ewels, available on GitHub.

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