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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
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<!-- Generated by graphviz version 2.38.0 (20140413.2041)
 -->
<!-- Title: snakemake_dag Pages: 1 -->
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<title>snakemake_dag</title>
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<g id="node1" class="node"><title>0</title>
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<text text-anchor="middle" x="1294" y="-15.5" font-family="sans" font-size="10.00">finish</text>
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<g id="node2" class="node"><title>1</title>
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<text text-anchor="middle" x="1294" y="-87.5" font-family="sans" font-size="10.00">MULTIQC_report</text>
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<g id="edge1" class="edge"><title>1&#45;&gt;0</title>
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<text text-anchor="middle" x="1294" y="-159.5" font-family="sans" font-size="10.00">prepare_MultiQC_config</text>
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<g id="edge2" class="edge"><title>2&#45;&gt;1</title>
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<g id="node4" class="node"><title>3</title>
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<text text-anchor="middle" x="1294" y="-237" font-family="sans" font-size="10.00">prepare_files_for_report</text>
<text text-anchor="middle" x="1294" y="-226" font-family="sans" font-size="10.00">output_dir: results</text>
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<g id="edge3" class="edge"><title>3&#45;&gt;2</title>
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<g id="node5" class="node"><title>4</title>
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<text text-anchor="middle" x="146" y="-309" font-family="sans" font-size="10.00">pe_fastqc</text>
<text text-anchor="middle" x="146" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<g id="edge4" class="edge"><title>4&#45;&gt;3</title>
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<text text-anchor="middle" x="462" y="-309" font-family="sans" font-size="10.00">fastqc</text>
<text text-anchor="middle" x="462" y="-298" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<text text-anchor="middle" x="759" y="-375.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<text text-anchor="middle" x="1210" y="-375.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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<g id="edge7" class="edge"><title>7&#45;&gt;3</title>
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<text text-anchor="middle" x="1430" y="-375.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
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<text text-anchor="middle" x="1085" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="1085" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<g id="edge9" class="edge"><title>9&#45;&gt;3</title>
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<text text-anchor="middle" x="1244" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="1244" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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<g id="edge10" class="edge"><title>10&#45;&gt;3</title>
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<text text-anchor="middle" x="748" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
<text text-anchor="middle" x="748" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<g id="edge11" class="edge"><title>11&#45;&gt;3</title>
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<text text-anchor="middle" x="921" y="-309" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
<text text-anchor="middle" x="921" y="-298" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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<g id="edge12" class="edge"><title>12&#45;&gt;3</title>
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<text text-anchor="middle" x="1343" y="-519.5" font-family="sans" font-size="10.00">star_rpm</text>
</g>
<!-- 13&#45;&gt;3 -->
<g id="edge13" class="edge"><title>13&#45;&gt;3</title>
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<text text-anchor="middle" x="1436" y="-447.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
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<!-- 13&#45;&gt;28 -->
<g id="edge56" class="edge"><title>13&#45;&gt;28</title>
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<text text-anchor="middle" x="1848" y="-519.5" font-family="sans" font-size="10.00">star_rpm</text>
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<!-- 14&#45;&gt;3 -->
<g id="edge14" class="edge"><title>14&#45;&gt;3</title>
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<text text-anchor="middle" x="1824" y="-447.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
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<!-- 14&#45;&gt;30 -->
<g id="edge58" class="edge"><title>14&#45;&gt;30</title>
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<g id="node16" class="node"><title>15</title>
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<text text-anchor="middle" x="1534" y="-375.5" font-family="sans" font-size="10.00">alfa_qc</text>
<!-- 15&#45;&gt;3 -->
<g id="edge15" class="edge"><title>15&#45;&gt;3</title>
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<!-- 22&#45;&gt;12 -->
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<!-- 23&#45;&gt;10 -->
<g id="edge26" class="edge"><title>23&#45;&gt;10</title>
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<g id="edge31" class="edge"><title>24&#45;&gt;13</title>
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<text text-anchor="middle" x="1343" y="-586" font-family="sans" font-size="10.00">seqmode: paired_end</text>
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<g id="edge52" class="edge"><title>24&#45;&gt;25</title>
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<g id="edge60" class="edge"><title>25&#45;&gt;34</title>
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<g id="edge55" class="edge"><title>26&#45;&gt;27</title>
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<g id="node36" class="node"><title>35</title>
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<text text-anchor="middle" x="1624" y="-519.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 26&#45;&gt;35 -->
<g id="edge62" class="edge"><title>26&#45;&gt;35</title>
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<!-- 27&#45;&gt;14 -->
<g id="edge34" class="edge"><title>27&#45;&gt;14</title>
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<!-- 27&#45;&gt;35 -->
<g id="edge63" class="edge"><title>27&#45;&gt;35</title>
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<!-- 28&#45;&gt;15 -->
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<g id="edge35" class="edge"><title>28&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1459.97,-431.876C1472.55,-422.893 1488.13,-411.763 1501.75,-402.034"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1503.83,-404.85 1509.93,-396.19 1499.76,-399.154 1503.83,-404.85"/>
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<!-- 29 -->
<g id="node30" class="node"><title>29</title>
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<path fill="none" stroke="#a7d856" stroke-width="2" d="M1729,-468C1729,-468 1649,-468 1649,-468 1643,-468 1637,-462 1637,-456 1637,-456 1637,-444 1637,-444 1637,-438 1643,-432 1649,-432 1649,-432 1729,-432 1729,-432 1735,-432 1741,-438 1741,-444 1741,-444 1741,-456 1741,-456 1741,-462 1735,-468 1729,-468"/>
<text text-anchor="middle" x="1689" y="-447.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
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<!-- 29&#45;&gt;15 -->
<g id="edge36" class="edge"><title>29&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1651.08,-431.876C1626.56,-420.799 1594.8,-406.457 1570.55,-395.504"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1571.87,-392.264 1561.32,-391.338 1568.99,-398.643 1571.87,-392.264"/>
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<!-- 29&#45;&gt;16 -->
<g id="edge38" class="edge"><title>29&#45;&gt;16</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1684.06,-431.697C1681.83,-423.898 1679.15,-414.509 1676.67,-405.829"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1680,-404.758 1673.89,-396.104 1673.27,-406.681 1680,-404.758"/>
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<!-- 30&#45;&gt;16 -->
<g id="edge37" class="edge"><title>30&#45;&gt;16</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1786.08,-431.876C1761.56,-420.799 1729.8,-406.457 1705.55,-395.504"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1706.87,-392.264 1696.32,-391.338 1703.99,-398.643 1706.87,-392.264"/>
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<!-- 31 -->
<g id="node32" class="node"><title>31</title>
<path fill="none" stroke="#88d856" stroke-width="2" d="M994,-833C994,-833 726,-833 726,-833 720,-833 714,-827 714,-821 714,-821 714,-809 714,-809 714,-803 720,-797 726,-797 726,-797 994,-797 994,-797 1000,-797 1006,-803 1006,-809 1006,-809 1006,-821 1006,-821 1006,-827 1000,-833 994,-833"/>
<text text-anchor="middle" x="860" y="-818" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="860" y="-807" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<!-- 31&#45;&gt;18 -->
<g id="edge41" class="edge"><title>31&#45;&gt;18</title>
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<path fill="none" stroke="grey" stroke-width="2" d="M860,-796.819C860,-788.422 860,-778.116 860,-768.686"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="863.5,-768.558 860,-758.558 856.5,-768.558 863.5,-768.558"/>
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<!-- 32 -->
<g id="node33" class="node"><title>32</title>
<path fill="none" stroke="#78d856" stroke-width="2" d="M1056.5,-540C1056.5,-540 955.5,-540 955.5,-540 949.5,-540 943.5,-534 943.5,-528 943.5,-528 943.5,-516 943.5,-516 943.5,-510 949.5,-504 955.5,-504 955.5,-504 1056.5,-504 1056.5,-504 1062.5,-504 1068.5,-510 1068.5,-516 1068.5,-516 1068.5,-528 1068.5,-528 1068.5,-534 1062.5,-540 1056.5,-540"/>
<text text-anchor="middle" x="1006" y="-525" font-family="sans" font-size="10.00">extract_transcriptome</text>
<text text-anchor="middle" x="1006" y="-514" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 32&#45;&gt;19 -->
<g id="edge42" class="edge"><title>32&#45;&gt;19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1021.82,-503.697C1029.57,-495.22 1039.04,-484.864 1047.52,-475.583"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1050.2,-477.846 1054.36,-468.104 1045.03,-473.123 1050.2,-477.846"/>
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<!-- 36 -->
<g id="node37" class="node"><title>36</title>
<path fill="none" stroke="#59d856" stroke-width="2" d="M985.5,-468C985.5,-468 900.5,-468 900.5,-468 894.5,-468 888.5,-462 888.5,-456 888.5,-456 888.5,-444 888.5,-444 888.5,-438 894.5,-432 900.5,-432 900.5,-432 985.5,-432 985.5,-432 991.5,-432 997.5,-438 997.5,-444 997.5,-444 997.5,-456 997.5,-456 997.5,-462 991.5,-468 985.5,-468"/>
<text text-anchor="middle" x="943" y="-453" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="943" y="-442" font-family="sans" font-size="10.00">kmer: 31</text>
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<!-- 32&#45;&gt;36 -->
<g id="edge65" class="edge"><title>32&#45;&gt;36</title>
<path fill="none" stroke="grey" stroke-width="2" d="M990.427,-503.697C982.798,-495.22 973.477,-484.864 965.124,-475.583"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="967.685,-473.196 958.394,-468.104 962.482,-477.879 967.685,-473.196"/>
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<!-- 33 -->
<g id="node34" class="node"><title>33</title>
<path fill="none" stroke="#56b9d8" stroke-width="2" d="M1330,-833C1330,-833 1050,-833 1050,-833 1044,-833 1038,-827 1038,-821 1038,-821 1038,-809 1038,-809 1038,-803 1044,-797 1050,-797 1050,-797 1330,-797 1330,-797 1336,-797 1342,-803 1342,-809 1342,-809 1342,-821 1342,-821 1342,-827 1336,-833 1330,-833"/>
<text text-anchor="middle" x="1190" y="-818" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="1190" y="-807" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<!-- 33&#45;&gt;20 -->
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<g id="edge43" class="edge"><title>33&#45;&gt;20</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1190,-796.819C1190,-788.422 1190,-778.116 1190,-768.686"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1193.5,-768.558 1190,-758.558 1186.5,-768.558 1193.5,-768.558"/>
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<!-- 34&#45;&gt;21 -->
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<g id="edge44" class="edge"><title>34&#45;&gt;21</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1498.99,-503.697C1510.81,-494.796 1525.39,-483.823 1538.18,-474.199"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1540.39,-476.915 1546.28,-468.104 1536.18,-471.322 1540.39,-476.915"/>
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<!-- 35&#45;&gt;21 -->
<g id="edge45" class="edge"><title>35&#45;&gt;21</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1610.4,-503.697C1603.88,-495.389 1595.93,-485.277 1588.75,-476.141"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1591.37,-473.805 1582.44,-468.104 1585.87,-478.13 1591.37,-473.805"/>
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<!-- 36&#45;&gt;22 -->
<g id="edge47" class="edge"><title>36&#45;&gt;22</title>
<path fill="none" stroke="grey" stroke-width="2" d="M938.303,-431.697C936.187,-423.898 933.638,-414.509 931.282,-405.829"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="934.64,-404.838 928.643,-396.104 927.884,-406.672 934.64,-404.838"/>
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<!-- 36&#45;&gt;23 -->
<g id="edge49" class="edge"><title>36&#45;&gt;23</title>
<path fill="none" stroke="grey" stroke-width="2" d="M971.866,-431.876C987.295,-422.724 1006.48,-411.342 1023.1,-401.485"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1025.21,-404.302 1032.02,-396.19 1021.64,-398.282 1025.21,-404.302"/>
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<!-- 37 -->
<g id="node38" class="node"><title>37</title>
<path fill="none" stroke="#56c9d8" stroke-width="2" d="M1767.5,-761C1767.5,-761 1666.5,-761 1666.5,-761 1660.5,-761 1654.5,-755 1654.5,-749 1654.5,-749 1654.5,-732 1654.5,-732 1654.5,-726 1660.5,-720 1666.5,-720 1666.5,-720 1767.5,-720 1767.5,-720 1773.5,-720 1779.5,-726 1779.5,-732 1779.5,-732 1779.5,-749 1779.5,-749 1779.5,-755 1773.5,-761 1767.5,-761"/>
<text text-anchor="middle" x="1717" y="-749" font-family="sans" font-size="10.00">create_index_star</text>
<text text-anchor="middle" x="1717" y="-738" font-family="sans" font-size="10.00">index_size: 75</text>
<text text-anchor="middle" x="1717" y="-727" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 37&#45;&gt;24 -->
<g id="edge50" class="edge"><title>37&#45;&gt;24</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1654.4,-727.365C1586.62,-714.225 1478.92,-693.349 1409.61,-679.913"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1410.16,-676.453 1399.67,-677.986 1408.82,-683.325 1410.16,-676.453"/>
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<!-- 37&#45;&gt;26 -->
<g id="edge53" class="edge"><title>37&#45;&gt;26</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1717,-719.689C1717,-711.907 1717,-702.842 1717,-694.447"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1720.5,-694.319 1717,-684.319 1713.5,-694.32 1720.5,-694.319"/>
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<!-- 37&#45;&gt;29 -->
<g id="edge57" class="edge"><title>37&#45;&gt;29</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1763.03,-719.97C1804.26,-699.684 1862.09,-663.634 1888,-612 1896.33,-595.398 1897.01,-518.975 1885,-504 1848.05,-457.922 1813.46,-481.709 1751.06,-468.017"/>
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<!-- 38 -->
<g id="node39" class="node"><title>38</title>
<path fill="none" stroke="#d6d856" stroke-width="2" d="M1619.5,-612C1619.5,-612 1498.5,-612 1498.5,-612 1492.5,-612 1486.5,-606 1486.5,-600 1486.5,-600 1486.5,-588 1486.5,-588 1486.5,-582 1492.5,-576 1498.5,-576 1498.5,-576 1619.5,-576 1619.5,-576 1625.5,-576 1631.5,-582 1631.5,-588 1631.5,-588 1631.5,-600 1631.5,-600 1631.5,-606 1625.5,-612 1619.5,-612"/>
<text text-anchor="middle" x="1559" y="-591.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
</g>
<!-- 38&#45;&gt;34 -->
<g id="edge61" class="edge"><title>38&#45;&gt;34</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1538.48,-575.697C1528.13,-566.965 1515.41,-556.24 1504.16,-546.75"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1506.18,-543.876 1496.28,-540.104 1501.67,-549.227 1506.18,-543.876"/>
</g>
<!-- 38&#45;&gt;35 -->
<g id="edge64" class="edge"><title>38&#45;&gt;35</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1575.07,-575.697C1582.94,-567.22 1592.56,-556.864 1601.17,-547.583"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1603.88,-549.814 1608.12,-540.104 1598.75,-545.051 1603.88,-549.814"/>
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</svg>