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        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 (c3cc50e)

        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

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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 v1.0.1, a tool for easy preprocessing of NGS data.

        Take a look at our docs for info about how to use this report to the fullest.

        Workflow
        rna-seq
        Date
        July 17, 2023
        Project
        rna
        Contact E-mail
        none@provided.com

        Report generated on 2023-07-18, 05:54 CEST based on data in:

        Change sample names:

        General Statistics

        Showing 185/185 rows and 14/29 columns.
        Sample Name% DuplicationM Reads After FilteringGC content% PF% AdapterInsert Size% Dups% MappedM Total seqs% Proper PairsM Total seqsGenome coverageM Genome readsM MT genome reads
        GSM1606175
        5.2%
        34.1
        44.9%
        96.9%
        1.0%
        172 bp
        9.1%
        100.0%
        32.8
        100.0%
        32.5
        1.7 X
        33.1
        0.4
        GSM1606176
        7.3%
        53.0
        45.1%
        97.4%
        1.0%
        172 bp
        11.9%
        100.0%
        50.6
        100.0%
        50.1
        2.7 X
        51.2
        0.6
        GSM1606177
        7.8%
        48.2
        44.9%
        90.5%
        0.9%
        169 bp
        10.3%
        100.0%
        45.3
        100.0%
        44.9
        2.4 X
        45.9
        0.5
        GSM1606178
        4.7%
        40.9
        44.8%
        97.4%
        0.9%
        169 bp
        8.4%
        100.0%
        39.6
        100.0%
        39.2
        2.1 X
        40.1
        0.4
        GSM1606179
        4.6%
        48.1
        44.7%
        97.7%
        1.0%
        167 bp
        8.4%
        100.0%
        46.5
        100.0%
        46.0
        2.5 X
        47.2
        0.4
        GSM1606180
        5.3%
        74.7
        44.6%
        97.7%
        0.8%
        168 bp
        9.8%
        100.0%
        72.6
        100.0%
        71.9
        3.9 X
        73.7
        0.7
        GSM1606181
        5.4%
        75.6
        44.5%
        97.3%
        0.8%
        163 bp
        10.1%
        100.0%
        73.7
        100.0%
        73.0
        3.9 X
        74.8
        0.6
        GSM1606182
        5.0%
        67.4
        44.4%
        97.3%
        0.8%
        169 bp
        9.3%
        100.0%
        65.6
        100.0%
        65.0
        3.5 X
        66.7
        0.6
        GSM1606183
        5.4%
        76.9
        44.5%
        92.3%
        1.0%
        162 bp
        9.5%
        100.0%
        74.5
        100.0%
        73.7
        4.0 X
        75.7
        0.7
        GSM1606184
        3.7%
        77.9
        44.4%
        97.1%
        0.8%
        163 bp
        7.8%
        100.0%
        76.1
        100.0%
        75.2
        4.0 X
        77.4
        0.6
        GSM1606185
        3.2%
        39.5
        44.5%
        97.0%
        1.0%
        160 bp
        5.9%
        100.0%
        38.4
        100.0%
        37.8
        2.1 X
        39.4
        0.3
        GSM1606186
        6.2%
        93.0
        44.4%
        97.1%
        1.1%
        158 bp
        11.1%
        100.0%
        90.2
        100.0%
        88.8
        4.9 X
        93.2
        0.9
        GSM1606187
        6.4%
        89.0
        44.6%
        97.3%
        1.1%
        159 bp
        11.1%
        100.0%
        86.1
        100.0%
        84.6
        4.7 X
        89.2
        0.9
        GSM1606188
        5.2%
        59.9
        44.7%
        97.5%
        1.0%
        162 bp
        9.2%
        100.0%
        57.9
        100.0%
        56.9
        3.1 X
        60.0
        0.6
        GSM1606189
        8.3%
        72.5
        44.8%
        84.9%
        0.8%
        164 bp
        11.4%
        100.0%
        67.5
        100.0%
        66.3
        3.7 X
        69.9
        0.9
        GSM1606190
        6.7%
        64.8
        44.8%
        96.5%
        1.0%
        164 bp
        11.7%
        100.0%
        62.3
        100.0%
        61.2
        3.4 X
        64.6
        0.8
        GSM1606191
        5.6%
        45.2
        45.0%
        97.1%
        1.0%
        166 bp
        9.9%
        100.0%
        43.5
        100.0%
        42.7
        2.4 X
        45.0
        0.7
        GSM1606192
        4.6%
        52.4
        45.1%
        97.4%
        1.1%
        168 bp
        9.8%
        100.0%
        50.6
        100.0%
        49.6
        2.7 X
        52.5
        0.9
        GSM1606193
        8.5%
        71.8
        44.9%
        97.2%
        1.0%
        167 bp
        14.7%
        100.0%
        69.2
        100.0%
        67.8
        3.8 X
        71.9
        1.1
        GSM1606194
        6.9%
        45.5
        44.9%
        97.3%
        1.1%
        164 bp
        12.1%
        100.0%
        43.9
        100.0%
        42.9
        2.4 X
        45.6
        0.8
        GSM1606195
        7.7%
        43.2
        45.0%
        87.3%
        0.9%
        167 bp
        11.8%
        100.0%
        40.4
        100.0%
        39.5
        2.2 X
        42.4
        0.5
        GSM1606196
        9.5%
        70.5
        44.8%
        96.9%
        1.1%
        163 bp
        16.1%
        100.0%
        67.8
        100.0%
        66.3
        3.7 X
        70.6
        1.3
        GSM1606197
        10.5%
        82.5
        44.9%
        97.1%
        1.1%
        165 bp
        17.7%
        100.0%
        79.7
        100.0%
        77.9
        4.4 X
        83.4
        1.4
        GSM1606198
        9.7%
        81.3
        45.0%
        97.1%
        1.1%
        171 bp
        16.4%
        100.0%
        78.6
        100.0%
        76.8
        4.3 X
        82.4
        1.0
        GSM1606199
        8.2%
        50.5
        44.8%
        97.1%
        1.5%
        150 bp
        14.4%
        100.0%
        48.9
        100.0%
        47.8
        2.7 X
        51.0
        1.0
        GSM1606200
        8.1%
        63.4
        44.9%
        97.1%
        0.7%
        164 bp
        14.2%
        100.0%
        61.4
        100.0%
        59.9
        3.4 X
        64.4
        1.1
        GSM1606201
        9.8%
        86.5
        45.0%
        92.1%
        0.7%
        163 bp
        16.5%
        100.0%
        83.1
        100.0%
        81.2
        4.5 X
        86.9
        1.6
        GSM1606202
        9.3%
        74.8
        44.9%
        96.8%
        0.8%
        161 bp
        15.7%
        100.0%
        72.3
        100.0%
        70.6
        4.0 X
        75.7
        1.4
        GSM1606203
        8.0%
        75.1
        44.8%
        97.2%
        0.8%
        162 bp
        14.4%
        100.0%
        72.9
        100.0%
        71.1
        4.0 X
        76.5
        1.3
        GSM1606204
        8.1%
        71.1
        44.8%
        97.3%
        0.7%
        163 bp
        14.3%
        100.0%
        69.1
        100.0%
        67.5
        3.8 X
        72.5
        1.3
        GSM1606205
        8.4%
        82.9
        44.8%
        97.2%
        0.7%
        166 bp
        14.7%
        100.0%
        80.6
        100.0%
        78.6
        4.4 X
        84.8
        1.4
        GSM1606206
        8.7%
        86.5
        44.8%
        97.3%
        0.7%
        162 bp
        15.1%
        100.0%
        84.2
        100.0%
        82.2
        4.6 X
        88.5
        1.5
        GSM1606207
        7.1%
        74.9
        45.0%
        94.6%
        0.7%
        167 bp
        12.9%
        100.0%
        72.6
        100.0%
        70.8
        4.0 X
        77.0
        0.9
        GSM1606208
        7.0%
        55.0
        44.9%
        97.1%
        0.8%
        160 bp
        12.1%
        100.0%
        53.4
        100.0%
        52.1
        3.0 X
        56.4
        0.6
        GSM1606209
        8.3%
        71.4
        44.9%
        97.3%
        0.9%
        158 bp
        14.1%
        100.0%
        69.4
        100.0%
        67.8
        3.8 X
        73.0
        1.1
        GSM1606210
        7.8%
        64.0
        44.9%
        97.3%
        0.9%
        159 bp
        13.3%
        100.0%
        62.2
        100.0%
        60.7
        3.4 X
        65.4
        0.9
        GSM1606211
        8.1%
        67.5
        44.9%
        97.3%
        0.9%
        158 bp
        13.8%
        100.0%
        65.7
        100.0%
        64.2
        3.6 X
        68.6
        1.2
        GSM1606212
        9.0%
        84.1
        44.9%
        97.4%
        0.9%
        158 bp
        15.0%
        100.0%
        81.7
        100.0%
        79.8
        4.5 X
        85.5
        1.5
        GSM1606213
        7.6%
        64.2
        44.8%
        95.0%
        0.8%
        159 bp
        13.0%
        100.0%
        62.3
        100.0%
        60.9
        3.4 X
        65.1
        1.0
        GSM1606214
        7.1%
        60.6
        44.8%
        97.2%
        0.8%
        160 bp
        12.5%
        100.0%
        59.1
        100.0%
        57.7
        3.2 X
        61.8
        0.9
        GSM1606215
        7.5%
        67.0
        44.9%
        97.5%
        0.8%
        160 bp
        13.0%
        100.0%
        65.4
        100.0%
        64.0
        3.6 X
        68.3
        1.1
        GSM1606216
        8.5%
        81.4
        45.0%
        97.2%
        0.8%
        160 bp
        14.5%
        100.0%
        79.4
        100.0%
        77.7
        4.3 X
        82.8
        1.3
        GSM1606217
        6.9%
        72.3
        44.7%
        96.5%
        0.8%
        157 bp
        13.0%
        100.0%
        70.5
        100.0%
        68.9
        3.9 X
        73.9
        0.8
        GSM1606218
        8.1%
        85.1
        44.8%
        96.7%
        0.8%
        158 bp
        14.7%
        100.0%
        82.9
        100.0%
        81.1
        4.6 X
        87.2
        0.7
        GSM1606219
        7.4%
        97.2
        44.6%
        93.5%
        0.7%
        166 bp
        14.5%
        100.0%
        94.9
        100.0%
        92.9
        5.1 X
        98.4
        1.8
        GSM1606220
        6.7%
        80.7
        44.6%
        96.1%
        0.7%
        165 bp
        13.2%
        100.0%
        78.8
        100.0%
        77.1
        4.3 X
        82.2
        1.3
        GSM1606221
        6.8%
        71.0
        44.7%
        96.6%
        0.7%
        163 bp
        13.0%
        100.0%
        69.4
        100.0%
        67.9
        3.8 X
        71.8
        1.4
        GSM1606222
        7.3%
        76.3
        44.5%
        96.6%
        0.7%
        161 bp
        13.7%
        100.0%
        74.6
        100.0%
        73.0
        4.1 X
        77.7
        1.1
        GSM1606223
        8.4%
        56.7
        44.8%
        96.0%
        0.6%
        178 bp
        14.1%
        100.0%
        55.6
        100.0%
        54.6
        3.0 X
        56.9
        1.1
        GSM1606224
        8.8%
        74.7
        44.8%
        96.6%
        3.5%
        153 bp
        15.9%
        100.0%
        72.8
        100.0%
        71.6
        3.9 X
        74.1
        1.8
        GSM1606225
        9.3%
        84.3
        44.6%
        96.7%
        3.4%
        151 bp
        16.4%
        100.0%
        81.9
        100.0%
        80.4
        4.4 X
        83.8
        1.9
        GSM1606226
        8.5%
        69.2
        44.6%
        96.5%
        3.3%
        152 bp
        15.3%
        100.0%
        67.3
        100.0%
        66.0
        3.6 X
        68.7
        1.7
        GSM1606227
        7.5%
        50.7
        45.0%
        96.4%
        3.1%
        156 bp
        14.0%
        100.0%
        49.5
        100.0%
        48.7
        2.6 X
        50.2
        1.2
        GSM1606228
        9.0%
        78.6
        44.8%
        96.5%
        3.1%
        153 bp
        16.2%
        100.0%
        76.7
        100.0%
        75.4
        4.1 X
        78.1
        1.9
        GSM1606229
        8.3%
        48.2
        45.6%
        96.6%
        2.8%
        165 bp
        15.4%
        100.0%
        47.0
        100.0%
        46.2
        2.5 X
        47.5
        1.3
        GSM1606230
        6.3%
        35.3
        45.2%
        96.9%
        2.8%
        160 bp
        11.9%
        100.0%
        34.5
        100.0%
        33.9
        1.8 X
        35.0
        0.9
        GSM1606231
        9.2%
        70.7
        45.0%
        97.0%
        2.7%
        162 bp
        16.4%
        100.0%
        69.1
        100.0%
        67.9
        3.6 X
        69.9
        2.0
        GSM1606232
        9.6%
        59.4
        45.8%
        96.8%
        3.7%
        168 bp
        17.1%
        100.0%
        57.8
        100.0%
        56.8
        3.1 X
        58.6
        1.5
        GSM1606233
        10.9%
        77.5
        45.4%
        96.7%
        2.8%
        164 bp
        19.1%
        100.0%
        75.3
        100.0%
        74.1
        3.9 X
        75.5
        2.8
        GSM1606234
        8.0%
        57.7
        44.7%
        97.0%
        3.3%
        154 bp
        14.4%
        100.0%
        56.4
        100.0%
        55.4
        3.0 X
        56.9
        2.0
        GSM1606235
        9.4%
        82.6
        44.9%
        97.0%
        2.7%
        162 bp
        16.9%
        100.0%
        80.7
        100.0%
        79.3
        4.2 X
        81.4
        2.8
        GSM1606236
        9.8%
        81.1
        45.0%
        96.2%
        2.7%
        161 bp
        18.1%
        100.0%
        79.2
        100.0%
        77.8
        4.2 X
        79.7
        2.9
        GSM1606237
        7.5%
        49.2
        45.1%
        96.3%
        2.6%
        162 bp
        14.8%
        100.0%
        48.1
        100.0%
        47.3
        2.5 X
        48.2
        1.9
        GSM1606238
        8.1%
        65.5
        44.5%
        96.4%
        2.7%
        155 bp
        15.3%
        100.0%
        64.1
        100.0%
        62.9
        3.4 X
        64.5
        2.5
        GSM1606239
        9.0%
        72.8
        44.7%
        96.2%
        3.0%
        153 bp
        16.7%
        100.0%
        71.3
        100.0%
        69.9
        3.7 X
        71.6
        2.8
        GSM1606240
        8.4%
        71.6
        44.4%
        96.4%
        3.8%
        150 bp
        15.6%
        100.0%
        70.0
        100.0%
        68.6
        3.7 X
        70.5
        2.8
        GSM1606241
        9.3%
        73.7
        45.2%
        96.2%
        2.9%
        156 bp
        17.2%
        100.0%
        71.7
        100.0%
        70.4
        3.7 X
        71.7
        3.0
        GSM1606242
        9.5%
        87.6
        44.5%
        95.6%
        2.8%
        156 bp
        17.2%
        100.0%
        83.7
        100.0%
        82.1
        4.4 X
        84.4
        3.5
        GSM1606243
        7.8%
        62.3
        44.4%
        96.4%
        3.1%
        151 bp
        14.7%
        100.0%
        60.7
        100.0%
        59.6
        3.2 X
        61.3
        2.4
        GSM1606244
        9.1%
        79.5
        44.8%
        96.2%
        3.3%
        151 bp
        16.8%
        100.0%
        77.5
        100.0%
        76.1
        4.1 X
        78.1
        2.8
        GSM1606245
        7.2%
        61.6
        44.3%
        96.1%
        3.0%
        152 bp
        13.9%
        100.0%
        60.1
        100.0%
        58.9
        3.2 X
        60.7
        2.4
        GSM1606246
        6.8%
        52.2
        44.4%
        96.3%
        2.9%
        153 bp
        13.0%
        100.0%
        50.9
        100.0%
        50.0
        2.7 X
        51.3
        2.0
        GSM1606247
        8.7%
        70.1
        44.5%
        95.9%
        4.9%
        156 bp
        16.9%
        100.0%
        66.5
        100.0%
        65.2
        3.5 X
        67.0
        2.7
        GSM1606248
        11.8%
        92.9
        44.9%
        96.8%
        3.8%
        157 bp
        20.2%
        100.0%
        90.9
        100.0%
        89.1
        4.7 X
        91.2
        3.7
        GSM1606249
        8.9%
        57.3
        45.1%
        96.7%
        3.5%
        158 bp
        16.4%
        100.0%
        56.1
        100.0%
        55.0
        2.9 X
        56.3
        2.2
        GSM1606250
        15.3%
        84.0
        47.2%
        96.2%
        3.8%
        184 bp
        26.9%
        100.0%
        81.3
        100.0%
        79.9
        4.2 X
        81.6
        2.9
        GSM1606251
        9.1%
        61.5
        45.2%
        96.4%
        3.3%
        158 bp
        16.5%
        100.0%
        60.0
        100.0%
        59.0
        3.1 X
        59.9
        2.7
        GSM1606252
        7.4%
        45.8
        45.0%
        96.5%
        2.7%
        168 bp
        13.9%
        100.0%
        44.7
        100.0%
        43.9
        2.3 X
        44.8
        1.9
        GSM1606253
        8.5%
        53.6
        45.1%
        96.7%
        3.4%
        159 bp
        15.6%
        100.0%
        52.5
        100.0%
        51.5
        2.7 X
        52.4
        2.3
        GSM1606254
        8.4%
        49.8
        45.1%
        96.7%
        3.3%
        158 bp
        15.4%
        100.0%
        48.7
        100.0%
        47.8
        2.5 X
        48.6
        2.1
        GSM1606255
        10.0%
        68.5
        45.2%
        96.7%
        4.0%
        154 bp
        17.7%
        100.0%
        66.9
        100.0%
        65.7
        3.5 X
        67.0
        2.8
        GSM1606256
        11.1%
        80.0
        45.4%
        96.7%
        3.4%
        150 bp
        19.3%
        100.0%
        78.1
        100.0%
        76.8
        4.1 X
        78.0
        3.4
        GSM1606257
        9.7%
        64.5
        45.0%
        96.5%
        3.4%
        154 bp
        17.3%
        100.0%
        63.0
        100.0%
        61.9
        3.2 X
        62.2
        3.4
        GSM1606258
        9.6%
        64.2
        45.1%
        96.7%
        3.3%
        152 bp
        17.2%
        100.0%
        62.8
        100.0%
        61.7
        3.2 X
        62.1
        3.3
        GSM1606259
        9.8%
        70.5
        44.6%
        96.8%
        3.5%
        149 bp
        17.1%
        100.0%
        69.0
        100.0%
        67.8
        3.6 X
        68.2
        3.9
        GSM1606260
        8.5%
        53.0
        44.9%
        96.9%
        3.8%
        148 bp
        15.0%
        100.0%
        51.7
        100.0%
        50.8
        2.7 X
        51.3
        2.5
        GSM1606261
        9.4%
        72.7
        44.4%
        97.1%
        3.4%
        148 bp
        16.3%
        100.0%
        71.2
        100.0%
        69.9
        3.7 X
        70.6
        3.7
        GSM1606262
        10.7%
        66.4
        45.5%
        96.8%
        3.3%
        152 bp
        18.5%
        100.0%
        64.9
        100.0%
        63.8
        3.4 X
        64.4
        3.1
        GSM1606263
        10.5%
        92.9
        44.6%
        96.8%
        3.6%
        148 bp
        17.9%
        100.0%
        90.9
        100.0%
        89.3
        4.7 X
        90.1
        4.8
        GSM1606264
        11.6%
        83.4
        45.3%
        96.9%
        3.7%
        149 bp
        19.7%
        100.0%
        81.4
        100.0%
        80.0
        4.2 X
        80.3
        4.4
        GSM1606265
        5.8%
        39.9
        45.0%
        72.1%
        0.5%
        183 bp
        14.5%
        100.0%
        38.4
        100.0%
        37.6
        2.1 X
        40.4
        0.5
        GSM1606266
        3.8%
        29.6
        45.0%
        72.2%
        0.5%
        202 bp
        9.6%
        100.0%
        28.5
        100.0%
        27.8
        1.6 X
        30.0
        0.2
        GSM1606267
        7.9%
        56.0
        46.0%
        72.3%
        0.5%
        192 bp
        18.3%
        100.0%
        54.5
        100.0%
        53.5
        2.9 X
        55.2
        1.5
        GSM1606268
        8.3%
        55.0
        46.2%
        71.8%
        0.6%
        194 bp
        19.5%
        100.0%
        53.3
        100.0%
        52.4
        2.8 X
        54.2
        1.3
        GSM1606269
        8.8%
        29.9
        47.5%
        72.0%
        0.6%
        216 bp
        20.9%
        100.0%
        29.1
        100.0%
        28.6
        1.5 X
        29.3
        1.0
        GSM1606270
        7.5%
        48.1
        45.8%
        72.7%
        0.6%
        178 bp
        17.5%
        100.0%
        47.0
        100.0%
        46.2
        2.4 X
        46.8
        2.2
        GSM1606319
        6.2%
        65.7
        45.5%
        95.3%
        0.5%
        182 bp
        18.5%
        100.0%
        63.7
        100.0%
        63.1
        3.4 X
        64.2
        0.9
        GSM1606320
        7.5%
        59.3
        46.1%
        95.0%
        0.5%
        180 bp
        22.2%
        100.0%
        56.9
        100.0%
        56.3
        3.0 X
        57.4
        0.9
        GSM1606321
        4.6%
        44.2
        45.4%
        95.2%
        0.6%
        174 bp
        14.1%
        100.0%
        42.7
        100.0%
        42.3
        2.3 X
        43.1
        0.6
        GSM1606322
        4.8%
        51.2
        45.1%
        94.8%
        0.6%
        172 bp
        14.8%
        100.0%
        49.5
        100.0%
        49.0
        2.6 X
        50.1
        0.6
        GSM1606323
        5.3%
        56.9
        45.7%
        95.2%
        0.5%
        176 bp
        16.0%
        100.0%
        55.1
        100.0%
        54.5
        2.9 X
        55.8
        0.7
        GSM1606324
        3.9%
        55.8
        45.0%
        95.7%
        0.5%
        174 bp
        11.8%
        100.0%
        54.2
        100.0%
        53.7
        2.9 X
        54.9
        0.6
        GSM1606325
        3.7%
        63.6
        44.9%
        93.0%
        0.6%
        166 bp
        13.6%
        100.0%
        61.9
        100.0%
        61.3
        3.3 X
        62.7
        0.6
        GSM1606326
        2.7%
        47.3
        44.4%
        93.4%
        0.6%
        161 bp
        10.5%
        100.0%
        46.3
        100.0%
        45.8
        2.4 X
        46.8
        0.5
        GSM1606327
        3.1%
        65.9
        44.6%
        93.2%
        0.5%
        167 bp
        11.4%
        100.0%
        64.3
        100.0%
        63.7
        3.4 X
        65.3
        0.5
        GSM1606328
        2.3%
        45.6
        44.3%
        92.7%
        0.5%
        165 bp
        8.8%
        100.0%
        44.4
        100.0%
        43.9
        2.4 X
        45.2
        0.4
        GSM1606329
        3.3%
        78.0
        44.4%
        93.3%
        0.6%
        163 bp
        12.0%
        100.0%
        76.2
        100.0%
        75.2
        4.1 X
        78.0
        0.6
        GSM1606330
        2.8%
        59.7
        44.6%
        93.4%
        0.6%
        162 bp
        10.2%
        100.0%
        58.0
        100.0%
        57.2
        3.1 X
        59.7
        0.5
        GSM1606331
        2.5%
        52.1
        44.4%
        92.4%
        0.5%
        164 bp
        9.7%
        100.0%
        50.5
        100.0%
        49.7
        2.7 X
        52.1
        0.5
        GSM1606332
        3.4%
        66.5
        44.3%
        92.1%
        0.6%
        163 bp
        12.8%
        100.0%
        64.3
        100.0%
        63.3
        3.5 X
        66.4
        0.7
        GSM1606333
        3.1%
        52.8
        44.6%
        92.4%
        0.7%
        160 bp
        11.6%
        100.0%
        51.2
        100.0%
        50.4
        2.8 X
        52.7
        0.6
        GSM1606334
        3.6%
        61.3
        44.5%
        91.6%
        0.6%
        164 bp
        13.9%
        100.0%
        59.4
        100.0%
        58.4
        3.2 X
        61.1
        0.8
        GSM1606335
        3.3%
        49.5
        44.6%
        92.2%
        0.5%
        167 bp
        12.7%
        100.0%
        48.0
        100.0%
        47.3
        2.6 X
        49.4
        0.7
        GSM1606336
        4.2%
        58.8
        44.6%
        92.5%
        0.5%
        171 bp
        15.5%
        100.0%
        57.2
        100.0%
        56.2
        3.1 X
        58.9
        0.9
        GSM1606337
        4.8%
        57.6
        44.7%
        90.6%
        0.5%
        167 bp
        16.0%
        100.0%
        55.5
        100.0%
        54.6
        3.0 X
        57.2
        0.8
        GSM1606338
        4.4%
        49.0
        44.7%
        90.5%
        0.6%
        166 bp
        15.0%
        100.0%
        47.2
        100.0%
        46.4
        2.5 X
        48.6
        0.7
        GSM1606339
        5.1%
        48.8
        44.8%
        90.8%
        0.6%
        164 bp
        16.4%
        100.0%
        46.8
        100.0%
        46.0
        2.5 X
        48.2
        0.7
        GSM1606340
        5.6%
        61.4
        44.9%
        89.8%
        0.6%
        163 bp
        18.4%
        100.0%
        59.0
        100.0%
        58.0
        3.2 X
        61.1
        0.6
        GSM1606341
        5.7%
        69.4
        44.8%
        90.6%
        0.6%
        162 bp
        18.5%
        100.0%
        66.9
        100.0%
        65.6
        3.6 X
        69.5
        0.9
        GSM1606342
        4.7%
        52.0
        44.7%
        90.9%
        0.5%
        162 bp
        15.4%
        100.0%
        50.2
        100.0%
        49.2
        2.7 X
        52.1
        0.7
        GSM1606343
        6.1%
        66.1
        44.9%
        92.1%
        0.6%
        168 bp
        18.2%
        100.0%
        64.2
        100.0%
        63.0
        3.5 X
        66.3
        1.0
        GSM1606344
        6.9%
        77.6
        44.9%
        92.1%
        0.6%
        165 bp
        20.0%
        100.0%
        75.3
        100.0%
        74.0
        4.1 X
        77.6
        1.2
        GSM1606345
        5.2%
        52.9
        45.0%
        92.1%
        0.6%
        166 bp
        15.8%
        100.0%
        51.3
        100.0%
        50.4
        2.8 X
        53.4
        0.5
        GSM1606346
        12.0%
        71.4
        45.5%
        97.5%
        0.8%
        170 bp
        19.2%
        100.0%
        69.4
        100.0%
        68.1
        3.8 X
        72.1
        0.8
        GSM1606347
        5.5%
        62.9
        44.8%
        92.1%
        0.6%
        166 bp
        16.7%
        100.0%
        61.2
        100.0%
        60.0
        3.3 X
        63.6
        0.8
        GSM1606348
        4.9%
        51.4
        44.8%
        92.5%
        0.6%
        164 bp
        14.8%
        100.0%
        50.0
        100.0%
        49.0
        2.7 X
        52.0
        0.7
        GSM1606349
        4.5%
        56.5
        44.6%
        89.8%
        0.6%
        161 bp
        15.9%
        100.0%
        54.8
        100.0%
        53.7
        3.0 X
        56.9
        0.8
        GSM1606350
        6.2%
        103.4
        44.8%
        89.5%
        0.6%
        161 bp
        20.3%
        100.0%
        100.3
        100.0%
        98.4
        5.4 X
        103.9
        1.2
        GSM1606351
        3.0%
        36.4
        44.5%
        90.3%
        0.5%
        160 bp
        11.1%
        100.0%
        35.3
        100.0%
        34.6
        1.9 X
        36.9
        0.4
        GSM1606352
        3.5%
        40.1
        44.8%
        88.8%
        0.5%
        166 bp
        12.8%
        100.0%
        38.8
        100.0%
        38.0
        2.1 X
        40.3
        0.4
        GSM1606353
        3.5%
        44.2
        44.5%
        89.6%
        0.6%
        162 bp
        12.7%
        100.0%
        42.8
        100.0%
        41.8
        2.3 X
        44.9
        0.5
        GSM1606354
        4.1%
        50.1
        45.0%
        89.9%
        0.6%
        164 bp
        14.3%
        100.0%
        48.6
        100.0%
        47.7
        2.6 X
        50.6
        0.3
        GSM1606355
        5.1%
        57.8
        45.0%
        91.0%
        0.6%
        166 bp
        15.5%
        100.0%
        56.3
        100.0%
        55.3
        3.1 X
        58.5
        0.5
        GSM1606356
        5.3%
        64.5
        44.8%
        90.9%
        0.6%
        164 bp
        15.9%
        100.0%
        62.9
        100.0%
        61.8
        3.4 X
        65.1
        0.7
        GSM1606357
        4.8%
        50.0
        44.8%
        91.3%
        0.5%
        164 bp
        14.5%
        100.0%
        48.8
        100.0%
        47.9
        2.6 X
        50.3
        0.6
        GSM1606358
        4.8%
        59.4
        44.9%
        90.3%
        0.5%
        164 bp
        15.4%
        100.0%
        58.0
        100.0%
        57.0
        3.1 X
        59.7
        0.7
        GSM1606359
        5.4%
        74.9
        44.8%
        90.9%
        0.5%
        165 bp
        16.7%
        100.0%
        73.0
        100.0%
        71.8
        3.9 X
        75.4
        0.8
        GSM1606360
        4.3%
        48.0
        45.0%
        91.2%
        0.6%
        166 bp
        13.2%
        100.0%
        46.9
        100.0%
        46.0
        2.5 X
        48.5
        0.5
        GSM1606361
        6.9%
        52.1
        44.8%
        95.0%
        0.6%
        172 bp
        16.3%
        100.0%
        50.9
        100.0%
        50.1
        2.8 X
        52.7
        0.4
        GSM1606362
        6.2%
        64.6
        45.0%
        94.8%
        0.6%
        170 bp
        14.9%
        100.0%
        63.3
        100.0%
        62.1
        3.4 X
        65.6
        0.7
        GSM1606363
        5.2%
        58.7
        44.7%
        94.7%
        0.6%
        171 bp
        12.9%
        100.0%
        57.4
        100.0%
        56.2
        3.1 X
        59.7
        0.8
        GSM1606364
        9.7%
        60.5
        44.7%
        94.4%
        0.5%
        191 bp
        22.8%
        100.0%
        59.3
        100.0%
        58.4
        3.2 X
        60.7
        0.6
        GSM1606365
        6.5%
        61.2
        45.4%
        94.8%
        0.5%
        174 bp
        15.6%
        100.0%
        59.9
        100.0%
        58.9
        3.2 X
        61.4
        1.0
        GSM1606366
        6.1%
        59.0
        45.1%
        95.1%
        0.6%
        170 bp
        14.7%
        100.0%
        57.8
        100.0%
        56.8
        3.1 X
        59.4
        1.0
        GSM1606367
        7.3%
        68.8
        45.5%
        94.2%
        0.6%
        178 bp
        18.0%
        100.0%
        67.4
        100.0%
        66.4
        3.6 X
        69.0
        1.1
        GSM919922
        5.8%
        20.6
        50.9%
        88.7%
        1.5%
        539 bp
        7.3%
        100.0%
        19.3
        100.0%
        18.9
        1.4 X
        20.4
        0.2
        GSM919923
        12.6%
        19.2
        50.1%
        88.4%
        1.3%
        588 bp
        9.1%
        100.0%
        16.6
        100.0%
        16.2
        1.2 X
        17.5
        0.2
        GSM919924
        9.9%
        20.1
        50.3%
        88.0%
        1.2%
        596 bp
        10.8%
        100.0%
        18.3
        100.0%
        17.9
        1.3 X
        19.3
        0.2
        GSM919925
        12.8%
        22.5
        49.9%
        88.7%
        0.9%
        589 bp
        18.2%
        100.0%
        20.9
        100.0%
        20.4
        1.5 X
        21.8
        0.4
        GSM919926
        7.8%
        22.5
        50.6%
        89.8%
        1.0%
        710 bp
        13.9%
        100.0%
        21.5
        100.0%
        20.8
        1.6 X
        22.9
        0.3
        GSM919927
        13.6%
        20.9
        49.8%
        89.3%
        1.0%
        682 bp
        15.1%
        100.0%
        18.7
        100.0%
        18.2
        1.4 X
        19.7
        0.2
        GSM919928
        10.1%
        21.1
        50.3%
        90.1%
        1.1%
        631 bp
        16.6%
        100.0%
        20.0
        100.0%
        19.5
        1.5 X
        21.1
        0.3
        GSM919929
        8.0%
        23.7
        50.7%
        90.3%
        1.2%
        707 bp
        14.2%
        100.0%
        22.7
        100.0%
        22.1
        1.7 X
        24.1
        0.3
        GSM919930
        10.2%
        19.8
        49.8%
        90.3%
        1.0%
        653 bp
        16.1%
        100.0%
        18.8
        100.0%
        18.4
        1.3 X
        19.3
        0.6
        GSM919931
        11.7%
        22.7
        50.1%
        90.2%
        1.0%
        622 bp
        17.3%
        100.0%
        21.4
        100.0%
        20.9
        1.5 X
        21.9
        0.6
        GSM919932
        8.0%
        24.5
        50.8%
        90.8%
        1.3%
        742 bp
        15.4%
        100.0%
        23.6
        100.0%
        23.0
        1.7 X
        24.6
        0.4
        GSM919933
        8.1%
        22.7
        50.7%
        91.0%
        1.2%
        795 bp
        15.1%
        100.0%
        21.9
        100.0%
        21.4
        1.6 X
        22.7
        0.4
        GSM919934
        8.4%
        22.1
        50.9%
        90.9%
        1.2%
        794 bp
        15.6%
        100.0%
        21.2
        100.0%
        20.8
        1.5 X
        21.9
        0.5
        GSM919935
        8.9%
        25.2
        50.7%
        91.4%
        1.1%
        818 bp
        16.5%
        100.0%
        24.2
        100.0%
        23.6
        1.7 X
        25.1
        0.5
        GSM919936
        9.0%
        22.2
        50.4%
        91.2%
        1.1%
        798 bp
        15.6%
        100.0%
        21.1
        100.0%
        20.6
        1.5 X
        21.7
        0.6
        GSM919937
        10.1%
        26.0
        50.6%
        91.4%
        1.0%
        817 bp
        17.1%
        100.0%
        24.5
        100.0%
        23.9
        1.8 X
        25.4
        0.7
        GSM919938
        4.1%
        20.8
        51.4%
        98.2%
        0.4%
        971 bp
        11.1%
        100.0%
        20.1
        100.0%
        19.7
        1.4 X
        20.7
        0.2
        GSM919939
        4.3%
        23.5
        51.4%
        98.3%
        0.4%
        956 bp
        11.6%
        100.0%
        22.7
        100.0%
        22.3
        1.6 X
        23.5
        0.2
        GSM919940
        3.8%
        20.4
        51.4%
        98.2%
        0.4%
        964 bp
        10.5%
        100.0%
        19.8
        100.0%
        19.5
        1.4 X
        20.5
        0.2
        GSM919941
        4.1%
        23.0
        51.2%
        98.2%
        0.4%
        967 bp
        11.2%
        100.0%
        22.3
        100.0%
        21.9
        1.6 X
        23.0
        0.3
        GSM919942
        3.8%
        21.7
        51.2%
        98.3%
        0.4%
        1012 bp
        10.2%
        100.0%
        21.1
        100.0%
        20.7
        1.5 X
        21.8
        0.3
        GSM919943
        3.5%
        22.6
        51.1%
        98.3%
        0.4%
        966 bp
        9.5%
        100.0%
        22.0
        100.0%
        21.6
        1.6 X
        22.7
        0.2
        GSM919944
        3.4%
        22.1
        50.8%
        98.3%
        0.5%
        864 bp
        9.0%
        100.0%
        21.3
        100.0%
        20.8
        1.5 X
        22.2
        0.3
        GSM919945
        4.2%
        20.5
        50.8%
        98.2%
        0.6%
        827 bp
        10.7%
        100.0%
        19.6
        100.0%
        19.1
        1.4 X
        20.5
        0.3
        GSM919946
        5.5%
        20.9
        50.9%
        98.2%
        0.6%
        792 bp
        13.7%
        100.0%
        20.0
        100.0%
        19.4
        1.4 X
        20.9
        0.4
        GSM919947
        6.2%
        19.3
        50.8%
        98.2%
        0.6%
        823 bp
        15.5%
        100.0%
        18.5
        100.0%
        18.0
        1.3 X
        19.3
        0.3
        GSM919948
        6.6%
        18.8
        50.8%
        98.2%
        0.5%
        796 bp
        16.0%
        100.0%
        18.0
        100.0%
        17.5
        1.3 X
        18.9
        0.3
        GSM919949
        8.1%
        25.5
        51.1%
        98.4%
        0.5%
        866 bp
        19.3%
        100.0%
        24.6
        100.0%
        23.9
        1.8 X
        25.8
        0.3
        GSM919950
        11.8%
        17.6
        50.5%
        98.8%
        0.5%
        820 bp
        18.3%
        100.0%
        16.8
        100.0%
        16.3
        1.2 X
        17.6
        0.4
        GSM919951
        13.4%
        22.6
        50.5%
        98.9%
        0.5%
        886 bp
        20.3%
        100.0%
        21.6
        100.0%
        21.1
        1.5 X
        22.3
        0.6
        GSM919952
        13.5%
        20.0
        50.4%
        98.8%
        0.5%
        865 bp
        20.9%
        100.0%
        19.2
        100.0%
        18.8
        1.4 X
        19.8
        0.6
        GSM919953
        14.2%
        20.1
        50.4%
        98.8%
        0.5%
        826 bp
        21.3%
        100.0%
        19.1
        100.0%
        18.6
        1.4 X
        19.9
        0.5
        GSM919954
        13.6%
        22.0
        50.5%
        98.9%
        0.5%
        854 bp
        20.7%
        100.0%
        21.1
        100.0%
        20.6
        1.5 X
        22.0
        0.4
        GSM919955
        15.3%
        22.0
        50.4%
        98.8%
        0.5%
        905 bp
        22.8%
        100.0%
        21.0
        100.0%
        20.5
        1.5 X
        21.6
        0.7
        GSM919956
        14.2%
        22.8
        51.2%
        98.9%
        0.5%
        927 bp
        20.9%
        100.0%
        21.5
        100.0%
        20.9
        1.5 X
        22.5
        0.3
        GSM919957
        15.3%
        24.3
        51.2%
        98.9%
        0.5%
        925 bp
        21.7%
        100.0%
        22.7
        100.0%
        22.1
        1.6 X
        23.8
        0.4
        GSM919958
        15.4%
        21.8
        51.0%
        98.9%
        0.5%
        939 bp
        21.6%
        100.0%
        20.3
        100.0%
        19.8
        1.5 X
        21.1
        0.5
        GSM919959
        16.7%
        22.8
        51.2%
        98.9%
        0.5%
        963 bp
        23.6%
        100.0%
        21.3
        100.0%
        20.8
        1.5 X
        22.3
        0.4
        GSM919960
        15.4%
        21.2
        51.3%
        98.9%
        0.5%
        949 bp
        21.3%
        100.0%
        19.7
        100.0%
        19.2
        1.4 X
        20.6
        0.4
        GSM919961
        15.6%
        20.6
        50.9%
        98.9%
        0.5%
        972 bp
        21.3%
        100.0%
        19.1
        100.0%
        18.7
        1.4 X
        19.9
        0.5

        Workflow explanation

        Preprocessing of reads was done automatically by seq2science v1.0.1 using the rna-seq workflow. Paired-end reads were trimmed with fastp v0.23.2 with default options. Genome assembly UCB_Xtro_10.0 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. Sample sequencing strandedness was inferred using RSeQC v5.0.1 in order to improve quantification accuracy. 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'. Read counting and summarizing to gene-level was performed on filtered bam using HTSeq-count v2.0.2. RNA-seq read duplication types were analyzed using dupRadar v1.28.0. The UCSC genome browser was used to visualize and inspect alignment. TPM normalized gene counts were generated using genomepy based on longest transcript lengths. Quality control metrics were aggregated by MultiQC v1.14.

        Assembly stats

        Genome assembly UCB_Xtro_10.0 contains of 167 contigs, with a GC-content of 40.73%, and 0.20% consists of the letter N. The N50-L50 stats are 153961319-5 and the N75-L75 stats are 147241510-7. The genome annotation contains 22689 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.

        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.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).

        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..

        SamTools post-sieve

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

        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).

        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.DOI: 10.1093/nar/gkw257.

        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.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).

        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 _brep hpf descriptive_name study
        GSM1606175 UCB_Xtro_10.0 stage1 0.0 ClutchA_polyA_0_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606319 UCB_Xtro_10.0 stage1 0.0 ClutchB_polyA_0_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606176 UCB_Xtro_10.0 stage1 0.5 ClutchA_polyA_0.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606320 UCB_Xtro_10.0 stage1 0.5 ClutchB_polyA_0.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919938 UCB_Xtro_10.0 stage1.5 1.0 Clutch2_2cell https://doi.org/10.1101/gr.141424.112
        GSM1606177 UCB_Xtro_10.0 stage2 1.0 ClutchA_polyA_1_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606321 UCB_Xtro_10.0 stage2 1.0 ClutchB_polyA_1_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919939 UCB_Xtro_10.0 stage2 1.33 Clutch2_4cell https://doi.org/10.1101/gr.141424.112
        GSM1606178 UCB_Xtro_10.0 stage3 1.5 ClutchA_polyA_1.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606322 UCB_Xtro_10.0 stage3 1.5 ClutchB_polyA_1.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919940 UCB_Xtro_10.0 stage2.5 1.67 Clutch2_8cell https://doi.org/10.1101/gr.141424.112
        GSM919941 UCB_Xtro_10.0 stage3 2.0 Clutch2_16cell https://doi.org/10.1101/gr.141424.112
        GSM1606179 UCB_Xtro_10.0 stage5 2.0 ClutchA_polyA_2_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606323 UCB_Xtro_10.0 stage5 2.0 ClutchB_polyA_2_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606180 UCB_Xtro_10.0 stage6 2.5 ClutchA_polyA_2.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606324 UCB_Xtro_10.0 stage6 2.5 ClutchB_polyA_2.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606181 UCB_Xtro_10.0 stage7 3.0 ClutchA_polyA_3_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606325 UCB_Xtro_10.0 stage7 3.0 ClutchB_polyA_3_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606182 UCB_Xtro_10.0 stage7 3.5 ClutchA_polyA_3.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606326 UCB_Xtro_10.0 stage7 3.5 ClutchB_polyA_3.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606183 UCB_Xtro_10.0 stage8 4.0 ClutchA_polyA_4_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606327 UCB_Xtro_10.0 stage8 4.0 ClutchB_polyA_4_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606184 UCB_Xtro_10.0 stage9 4.5 ClutchA_polyA_4.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606328 UCB_Xtro_10.0 stage9 4.5 ClutchB_polyA_4.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606185 UCB_Xtro_10.0 stage9 5.0 ClutchA_polyA_5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606329 UCB_Xtro_10.0 stage9 5.0 ClutchB_polyA_5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606186 UCB_Xtro_10.0 stage9 5.5 ClutchA_polyA_5.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606330 UCB_Xtro_10.0 stage9 5.5 ClutchB_polyA_5.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606187 UCB_Xtro_10.0 stage9 6.0 ClutchA_polyA_6_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606331 UCB_Xtro_10.0 stage9 6.0 ClutchB_polyA_6_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919923 UCB_Xtro_10.0 stage10 6.5 Clutch1_Stage10 https://doi.org/10.1101/gr.141424.112
        GSM919945 UCB_Xtro_10.0 stage10 6.5 Clutch2_Stage10 https://doi.org/10.1101/gr.141424.112
        GSM1606188 UCB_Xtro_10.0 stage10 6.5 ClutchA_polyA_6.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606332 UCB_Xtro_10.0 stage10 6.5 ClutchB_polyA_6.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606189 UCB_Xtro_10.0 stage10 7.0 ClutchA_polyA_7_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606333 UCB_Xtro_10.0 stage10 7.0 ClutchB_polyA_7_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606190 UCB_Xtro_10.0 stage10 7.5 ClutchA_polyA_7.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606334 UCB_Xtro_10.0 stage10 7.5 ClutchB_polyA_7.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919924 UCB_Xtro_10.0 stage11 8.0 Clutch1_Stage11-12_Set1 https://doi.org/10.1101/gr.141424.112
        GSM919925 UCB_Xtro_10.0 stage11 8.0 Clutch1_Stage11-12_Set2 https://doi.org/10.1101/gr.141424.112
        GSM919946 UCB_Xtro_10.0 stage11 8.0 Clutch2_Stage11-12 https://doi.org/10.1101/gr.141424.112
        GSM1606191 UCB_Xtro_10.0 stage11 8.0 ClutchA_polyA_8_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606335 UCB_Xtro_10.0 stage11 8.0 ClutchB_polyA_8_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606192 UCB_Xtro_10.0 stage12 8.5 ClutchA_polyA_8.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606336 UCB_Xtro_10.0 stage12 8.5 ClutchB_polyA_8.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606193 UCB_Xtro_10.0 stage12 9.0 ClutchA_polyA_9_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606337 UCB_Xtro_10.0 stage12 9.0 ClutchB_polyA_9_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606194 UCB_Xtro_10.0 stage12 9.5 ClutchA_polyA_9.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606338 UCB_Xtro_10.0 stage12 9.5 ClutchB_polyA_9.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606195 UCB_Xtro_10.0 stage12 10.0 ClutchA_polyA_10_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606339 UCB_Xtro_10.0 stage12 10.0 ClutchB_polyA_10_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606196 UCB_Xtro_10.0 stage12.5 10.5 ClutchA_polyA_10.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606340 UCB_Xtro_10.0 stage12.5 10.5 ClutchB_polyA_10.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606197 UCB_Xtro_10.0 stage12.5 11.0 ClutchA_polyA_11_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606341 UCB_Xtro_10.0 stage12.5 11.0 ClutchB_polyA_11_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606198 UCB_Xtro_10.0 stage12.5 11.5 ClutchA_polyA_11.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606265 UCB_Xtro_10.0 stage12.5 11.5 ClutchA_polyA_11.5_hpf_repeat https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606342 UCB_Xtro_10.0 stage12.5 11.5 ClutchB_polyA_11.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919947 UCB_Xtro_10.0 stage13 12.0 Clutch2_Stage13-14_Set1 https://doi.org/10.1101/gr.141424.112
        GSM919948 UCB_Xtro_10.0 stage13 12.0 Clutch2_Stage13-14_Set2 https://doi.org/10.1101/gr.141424.112
        GSM1606199 UCB_Xtro_10.0 stage13 12.0 ClutchA_polyA_12_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606343 UCB_Xtro_10.0 stage13 12.0 ClutchB_polyA_12_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606200 UCB_Xtro_10.0 stage13 12.5 ClutchA_polyA_12.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606344 UCB_Xtro_10.0 stage13 12.5 ClutchB_polyA_12.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606201 UCB_Xtro_10.0 stage13 13.0 ClutchA_polyA_13_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606345 UCB_Xtro_10.0 stage13 13.0 ClutchB_polyA_13_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606202 UCB_Xtro_10.0 stage14 13.5 ClutchA_polyA_13.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606346 UCB_Xtro_10.0 stage14 13.5 ClutchB_polyA_13.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606203 UCB_Xtro_10.0 stage14 14.0 ClutchA_polyA_14_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606347 UCB_Xtro_10.0 stage14 14.0 ClutchB_polyA_14_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919926 UCB_Xtro_10.0 stage15 14.5 Clutch1_Stage15 https://doi.org/10.1101/gr.141424.112
        GSM1606204 UCB_Xtro_10.0 stage15 14.5 ClutchA_polyA_14.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606348 UCB_Xtro_10.0 stage15 14.5 ClutchB_polyA_14.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919927 UCB_Xtro_10.0 stage16 15.0 Clutch1_Stage16-18 https://doi.org/10.1101/gr.141424.112
        GSM919949 UCB_Xtro_10.0 stage16 15.0 Clutch2_Stage16-18 https://doi.org/10.1101/gr.141424.112
        GSM1606205 UCB_Xtro_10.0 stage17 15.0 ClutchA_polyA_15_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606349 UCB_Xtro_10.0 stage17 15.0 ClutchB_polyA_15_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919928 UCB_Xtro_10.0 stage19 15.5 Clutch1_Stage19_Set1 https://doi.org/10.1101/gr.141424.112
        GSM919929 UCB_Xtro_10.0 stage19 15.5 Clutch1_Stage19_Set2 https://doi.org/10.1101/gr.141424.112
        GSM919950 UCB_Xtro_10.0 stage19 15.5 Clutch2_Stage19 https://doi.org/10.1101/gr.141424.112
        GSM1606206 UCB_Xtro_10.0 stage19 15.5 ClutchA_polyA_15.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606350 UCB_Xtro_10.0 stage19 15.5 ClutchB_polyA_15.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919930 UCB_Xtro_10.0 stage20 16.0 Clutch1_Stage20-21 https://doi.org/10.1101/gr.141424.112
        GSM919951 UCB_Xtro_10.0 stage20 16.0 Clutch2_Stage20-21 https://doi.org/10.1101/gr.141424.112
        GSM1606207 UCB_Xtro_10.0 stage20 16.0 ClutchA_polyA_16_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606351 UCB_Xtro_10.0 stage20 16.0 ClutchB_polyA_16_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606208 UCB_Xtro_10.0 stage21 16.5 ClutchA_polyA_16.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606352 UCB_Xtro_10.0 stage21 16.5 ClutchB_polyA_16.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606209 UCB_Xtro_10.0 stage21 17.0 ClutchA_polyA_17_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606353 UCB_Xtro_10.0 stage21 17.0 ClutchB_polyA_17_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919931 UCB_Xtro_10.0 stage22 17.5 Clutch1_Stage22-23 https://doi.org/10.1101/gr.141424.112
        GSM919952 UCB_Xtro_10.0 stage22 17.5 Clutch2_Stage22-23 https://doi.org/10.1101/gr.141424.112
        GSM1606210 UCB_Xtro_10.0 stage22 17.5 ClutchA_polyA_17.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606354 UCB_Xtro_10.0 stage22 17.5 ClutchB_polyA_17.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606211 UCB_Xtro_10.0 stage22 18.0 ClutchA_polyA_18_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606355 UCB_Xtro_10.0 stage22 18.0 ClutchB_polyA_18_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606212 UCB_Xtro_10.0 stage23 18.5 ClutchA_polyA_18.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606356 UCB_Xtro_10.0 stage23 18.5 ClutchB_polyA_18.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919932 UCB_Xtro_10.0 stage24 19.0 Clutch1_Stage24-26 https://doi.org/10.1101/gr.141424.112
        GSM919953 UCB_Xtro_10.0 stage24 19.0 Clutch2_Stage24-26_Set1 https://doi.org/10.1101/gr.141424.112
        GSM919954 UCB_Xtro_10.0 stage24 19.0 Clutch2_Stage24-26_Set2 https://doi.org/10.1101/gr.141424.112
        GSM1606213 UCB_Xtro_10.0 stage24 19.0 ClutchA_polyA_19_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606357 UCB_Xtro_10.0 stage24 19.0 ClutchB_polyA_19_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606214 UCB_Xtro_10.0 stage24 19.5 ClutchA_polyA_19.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606358 UCB_Xtro_10.0 stage24 19.5 ClutchB_polyA_19.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606215 UCB_Xtro_10.0 stage24 20.0 ClutchA_polyA_20_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606359 UCB_Xtro_10.0 stage24 20.0 ClutchB_polyA_20_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606216 UCB_Xtro_10.0 stage24 20.5 ClutchA_polyA_20.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606360 UCB_Xtro_10.0 stage24 20.5 ClutchB_polyA_20.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606217 UCB_Xtro_10.0 stage25 21.0 ClutchA_polyA_21_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606361 UCB_Xtro_10.0 stage25 21.0 ClutchB_polyA_21_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606218 UCB_Xtro_10.0 stage25 21.5 ClutchA_polyA_21.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606266 UCB_Xtro_10.0 stage25 21.5 ClutchA_polyA_21.5_hpf_repeat https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606362 UCB_Xtro_10.0 stage25 21.5 ClutchB_polyA_21.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606219 UCB_Xtro_10.0 stage25 22.0 ClutchA_polyA_22_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606363 UCB_Xtro_10.0 stage25 22.0 ClutchB_polyA_22_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606220 UCB_Xtro_10.0 stage26 22.5 ClutchA_polyA_22.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606364 UCB_Xtro_10.0 stage26 22.5 ClutchB_polyA_22.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606221 UCB_Xtro_10.0 stage26 23.0 ClutchA_polyA_23_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606365 UCB_Xtro_10.0 stage26 23.0 ClutchB_polyA_23_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606222 UCB_Xtro_10.0 stage26 23.5 ClutchA_polyA_23.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606366 UCB_Xtro_10.0 stage26 23.5 ClutchB_polyA_23.5_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606223 UCB_Xtro_10.0 stage27 24.0 ClutchA_polyA_24_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606367 UCB_Xtro_10.0 stage27 24.0 ClutchB_polyA_24_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606224 UCB_Xtro_10.0 stage27 25.0 ClutchA_polyA_25_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606225 UCB_Xtro_10.0 stage27 26.0 ClutchA_polyA_26_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919933 UCB_Xtro_10.0 stage28 27.0 Clutch1_Stage28 https://doi.org/10.1101/gr.141424.112
        GSM919955 UCB_Xtro_10.0 stage28 27.0 Clutch2_Stage28 https://doi.org/10.1101/gr.141424.112
        GSM1606226 UCB_Xtro_10.0 stage28 27.0 ClutchA_polyA_27_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606227 UCB_Xtro_10.0 stage28 28.0 ClutchA_polyA_28_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606228 UCB_Xtro_10.0 stage30 29.0 ClutchA_polyA_29_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919934 UCB_Xtro_10.0 stage31 30.0 Clutch1_Stage31-32 https://doi.org/10.1101/gr.141424.112
        GSM919956 UCB_Xtro_10.0 stage31 30.0 Clutch2_Stage31-32 https://doi.org/10.1101/gr.141424.112
        GSM1606229 UCB_Xtro_10.0 stage31 30.0 ClutchA_polyA_30_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606267 UCB_Xtro_10.0 stage31 30.0 ClutchA_polyA_30_hpf_repeat https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606230 UCB_Xtro_10.0 stage32 31.0 ClutchA_polyA_31_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606231 UCB_Xtro_10.0 stage32 32.0 ClutchA_polyA_32_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919935 UCB_Xtro_10.0 stage33 33.0 Clutch1_Stage33-34 https://doi.org/10.1101/gr.141424.112
        GSM919957 UCB_Xtro_10.0 stage33 33.0 Clutch2_Stage33-34 https://doi.org/10.1101/gr.141424.112
        GSM1606232 UCB_Xtro_10.0 stage34 33.0 ClutchA_polyA_33_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606268 UCB_Xtro_10.0 stage34 33.0 ClutchA_polyA_33_hpf_repeat https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606233 UCB_Xtro_10.0 stage34 34.0 ClutchA_polyA_34_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606234 UCB_Xtro_10.0 stage34 35.0 ClutchA_polyA_35_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606235 UCB_Xtro_10.0 stage35 36.0 ClutchA_polyA_36_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606236 UCB_Xtro_10.0 stage36 37.0 ClutchA_polyA_37_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606237 UCB_Xtro_10.0 stage37 38.0 ClutchA_polyA_38_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919958 UCB_Xtro_10.0 stage38 39.0 Clutch2_Stage38-39 https://doi.org/10.1101/gr.141424.112
        GSM1606238 UCB_Xtro_10.0 stage38 39.0 ClutchA_polyA_39_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606239 UCB_Xtro_10.0 stage38 40.0 ClutchA_polyA_40_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606240 UCB_Xtro_10.0 stage39 41.0 ClutchA_polyA_41_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606241 UCB_Xtro_10.0 stage39 42.0 ClutchA_polyA_42_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606242 UCB_Xtro_10.0 stage39 44.0 ClutchA_polyA_44_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606243 UCB_Xtro_10.0 stage39 45.0 ClutchA_polyA_45_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919936 UCB_Xtro_10.0 stage40 46.0 Clutch1_Stage40 https://doi.org/10.1101/gr.141424.112
        GSM919959 UCB_Xtro_10.0 stage40 46.0 Clutch2_Stage40 https://doi.org/10.1101/gr.141424.112
        GSM1606244 UCB_Xtro_10.0 stage40 46.0 ClutchA_polyA_46_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606245 UCB_Xtro_10.0 stage40 47.0 ClutchA_polyA_47_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606246 UCB_Xtro_10.0 stage40 48.0 ClutchA_polyA_48_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606247 UCB_Xtro_10.0 stage40 49.0 ClutchA_polyA_49_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606248 UCB_Xtro_10.0 stage40 50.0 ClutchA_polyA_50_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919937 UCB_Xtro_10.0 stage41 51.0 Clutch1_Stage41-42 https://doi.org/10.1101/gr.141424.112
        GSM919960 UCB_Xtro_10.0 stage41 51.0 Clutch2_Stage41-42 https://doi.org/10.1101/gr.141424.112
        GSM1606249 UCB_Xtro_10.0 stage41 51.0 ClutchA_polyA_51_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606250 UCB_Xtro_10.0 stage41 52.0 ClutchA_polyA_52_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606269 UCB_Xtro_10.0 stage41 52.0 ClutchA_polyA_52_hpf_repeat https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606251 UCB_Xtro_10.0 stage41 53.0 ClutchA_polyA_53_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606252 UCB_Xtro_10.0 stage41 54.0 ClutchA_polyA_54_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606253 UCB_Xtro_10.0 stage41 55.0 ClutchA_polyA_55_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM919922 UCB_Xtro_10.0 stage9 56.0 Clutch1_Stage9 https://doi.org/10.1101/gr.141424.112
        GSM919961 UCB_Xtro_10.0 stage44 56.0 Clutch2_Stage44-45 https://doi.org/10.1101/gr.141424.112
        GSM919942 UCB_Xtro_10.0 stage6 56.0 Clutch2_Stage6 https://doi.org/10.1101/gr.141424.112
        GSM919943 UCB_Xtro_10.0 stage8 56.0 Clutch2_Stage8 https://doi.org/10.1101/gr.141424.112
        GSM919944 UCB_Xtro_10.0 stage9 56.0 Clutch2_Stage9 https://doi.org/10.1101/gr.141424.112
        GSM1606254 UCB_Xtro_10.0 stage42 56.0 ClutchA_polyA_56_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606255 UCB_Xtro_10.0 stage42 57.0 ClutchA_polyA_57_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606256 UCB_Xtro_10.0 stage42 58.0 ClutchA_polyA_58_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606257 UCB_Xtro_10.0 stage42 59.0 ClutchA_polyA_59_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606258 UCB_Xtro_10.0 stage42 60.0 ClutchA_polyA_60_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606259 UCB_Xtro_10.0 stage42 61.0 ClutchA_polyA_61_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606260 UCB_Xtro_10.0 stage42 62.0 ClutchA_polyA_62_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606261 UCB_Xtro_10.0 stage42 63.0 ClutchA_polyA_63_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606262 UCB_Xtro_10.0 stage42 64.0 ClutchA_polyA_64_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606270 UCB_Xtro_10.0 stage42 64.0 ClutchA_polyA_64_hpf_repeat https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606263 UCB_Xtro_10.0 stage42 65.0 ClutchA_polyA_65_hpf https://doi.org/10.1016/j.celrep.2015.12.050
        GSM1606264 UCB_Xtro_10.0 stage42 66.0 ClutchA_polyA_66_hpf https://doi.org/10.1016/j.celrep.2015.12.050

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

# pipeline file locations
result_dir: .  # where to store results
genome_dir: /bank/genomes  # where to look for or download the genomes
fastq_dir: /bank/experiments/2022-04-bsc/xt/fastq  # where to look for or download the fastqs


# 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

# 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)

# should the final output be stored as cram files (instead of bam) to save storage?
store_as_cram: false

        MultiQC v1.14 (c3cc50e) - Written by Phil Ewels, available on GitHub.

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