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<!-- Title: snakemake_dag Pages: 1 -->
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<!-- 1 -->
<g id="node2" class="node"><title>1</title>
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<!-- 1&#45;&gt;0 -->
<g id="edge3" class="edge"><title>1&#45;&gt;0</title>
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<text text-anchor="middle" x="114" y="-87.5" font-family="sans" font-size="10.00">fastqc</text>
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<!-- 2&#45;&gt;0 -->
<g id="edge4" class="edge"><title>2&#45;&gt;0</title>
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<!-- 3 -->
<g id="node4" class="node"><title>3</title>
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<text text-anchor="middle" x="83" y="-447.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<!-- 3&#45;&gt;0 -->
<g id="edge8" class="edge"><title>3&#45;&gt;0</title>
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<!-- 4 -->
<g id="node5" class="node"><title>4</title>
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<text text-anchor="middle" x="259" y="-447.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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<!-- 4&#45;&gt;0 -->
<g id="edge6" class="edge"><title>4&#45;&gt;0</title>
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<!-- 5 -->
<g id="node6" class="node"><title>5</title>
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<text text-anchor="middle" x="478" y="-159.5" font-family="sans" font-size="10.00">plot_TIN_scores</text>
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<!-- 5&#45;&gt;0 -->
<g id="edge9" class="edge"><title>5&#45;&gt;0</title>
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<!-- 6 -->
<g id="node7" class="node"><title>6</title>
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<text text-anchor="middle" x="303" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
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<!-- 6&#45;&gt;0 -->
<g id="edge7" class="edge"><title>6&#45;&gt;0</title>
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<!-- 7 -->
<g id="node8" class="node"><title>7</title>
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<text text-anchor="middle" x="467" y="-375.5" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
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<!-- 7&#45;&gt;0 -->
<g id="edge1" class="edge"><title>7&#45;&gt;0</title>
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<!-- 8 -->
<g id="node9" class="node"><title>8</title>
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<!-- 8&#45;&gt;0 -->
<g id="edge10" class="edge"><title>8&#45;&gt;0</title>
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<!-- 20 -->
<g id="node21" class="node"><title>20</title>
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<text text-anchor="middle" x="850" y="-231.5" font-family="sans" font-size="10.00">rename_star_rpm_for_alfa</text>
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<!-- 8&#45;&gt;20 -->
<g id="edge40" class="edge"><title>8&#45;&gt;20</title>
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<!-- 9 -->
<g id="node10" class="node"><title>9</title>
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<text text-anchor="middle" x="835" y="-159.5" font-family="sans" font-size="10.00">alfa_qc</text>
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<!-- 9&#45;&gt;0 -->
<g id="edge5" class="edge"><title>9&#45;&gt;0</title>
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<!-- 10 -->
<g id="node11" class="node"><title>10</title>
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<text text-anchor="middle" x="806" y="-87.5" font-family="sans" font-size="10.00">alfa_qc_all_samples</text>
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<!-- 9&#45;&gt;10 -->
<g id="edge25" class="edge"><title>9&#45;&gt;10</title>
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<!-- 10&#45;&gt;0 -->
<g id="edge2" class="edge"><title>10&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M753.403,-75.7453C747.22,-74.3834 740.984,-73.0989 735,-72 598.087,-46.8556 433.355,-29.4441 361.065,-22.4398"/>
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<!-- 11 -->
<g id="node12" class="node"><title>11</title>
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<text text-anchor="middle" x="339" y="-519.5" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
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<!-- 11&#45;&gt;3 -->
<g id="edge11" class="edge"><title>11&#45;&gt;3</title>
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<!-- 15 -->
<g id="node16" class="node"><title>15</title>
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<text text-anchor="middle" x="416" y="-447.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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<!-- 11&#45;&gt;15 -->
<g id="edge31" class="edge"><title>11&#45;&gt;15</title>
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<!-- 17 -->
<g id="node18" class="node"><title>17</title>
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<!-- 11&#45;&gt;17 -->
<g id="edge35" class="edge"><title>11&#45;&gt;17</title>
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<!-- 12 -->
<g id="node13" class="node"><title>12</title>
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<!-- 12&#45;&gt;3 -->
<g id="edge12" class="edge"><title>12&#45;&gt;3</title>
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<!-- 12&#45;&gt;4 -->
<g id="edge14" class="edge"><title>12&#45;&gt;4</title>
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<!-- 13 -->
<g id="node14" class="node"><title>13</title>
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<!-- 13&#45;&gt;4 -->
<g id="edge13" class="edge"><title>13&#45;&gt;4</title>
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<!-- 16 -->
<g id="node17" class="node"><title>16</title>
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<!-- 13&#45;&gt;16 -->
<g id="edge33" class="edge"><title>13&#45;&gt;16</title>
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<!-- 19 -->
<g id="node20" class="node"><title>19</title>
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<!-- 13&#45;&gt;19 -->
<g id="edge39" class="edge"><title>13&#45;&gt;19</title>
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<!-- 14 -->
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<!-- 14&#45;&gt;5 -->
<g id="edge15" class="edge"><title>14&#45;&gt;5</title>
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<!-- 15&#45;&gt;6 -->
<g id="edge16" class="edge"><title>15&#45;&gt;6</title>
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<!-- 15&#45;&gt;7 -->
<g id="edge18" class="edge"><title>15&#45;&gt;7</title>
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<!-- 16&#45;&gt;6 -->
<g id="edge17" class="edge"><title>16&#45;&gt;6</title>
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<!-- 16&#45;&gt;7 -->
<g id="edge19" class="edge"><title>16&#45;&gt;7</title>
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<!-- 17&#45;&gt;8 -->
<g id="edge20" class="edge"><title>17&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M899.722,-433.313C918.045,-425.265 936.359,-413.365 947,-396 955.359,-382.357 955.132,-373.779 947,-360 934.386,-338.628 909.727,-325.279 888.56,-317.324"/>
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<!-- 18 -->
<g id="node19" class="node"><title>18</title>
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<text text-anchor="middle" x="851" y="-375.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
</g>
<!-- 17&#45;&gt;18 -->
<g id="edge36" class="edge"><title>17&#45;&gt;18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M844.978,-431.697C845.859,-423.983 846.919,-414.712 847.901,-406.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="851.387,-406.437 849.045,-396.104 844.432,-405.642 851.387,-406.437"/>
</g>
<!-- 25 -->
<g id="node26" class="node"><title>25</title>
<path fill="none" stroke="#56a2d8" stroke-width="2" d="M780,-324C780,-324 692,-324 692,-324 686,-324 680,-318 680,-312 680,-312 680,-300 680,-300 680,-294 686,-288 692,-288 692,-288 780,-288 780,-288 786,-288 792,-294 792,-300 792,-300 792,-312 792,-312 792,-318 786,-324 780,-324"/>
<text text-anchor="middle" x="736" y="-303.5" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
</g>
<!-- 17&#45;&gt;25 -->
<g id="edge42" class="edge"><title>17&#45;&gt;25</title>
<path fill="none" stroke="grey" stroke-width="2" d="M799.53,-431.827C783.272,-423.345 766.08,-411.537 755,-396 742.133,-377.959 737.662,-352.972 736.249,-334.065"/>
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<!-- 18&#45;&gt;8 -->
<g id="edge21" class="edge"><title>18&#45;&gt;8</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="854.5,-334.104 851,-324.104 847.5,-334.104 854.5,-334.104"/>
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<!-- 18&#45;&gt;25 -->
<g id="edge44" class="edge"><title>18&#45;&gt;25</title>
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<!-- 19&#45;&gt;8 -->
<g id="edge22" class="edge"><title>19&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M970.876,-431.724C975.205,-412.573 978.916,-381.548 965,-360 948.17,-333.94 914.888,-320.48 888.609,-313.662"/>
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<!-- 19&#45;&gt;18 -->
<g id="edge37" class="edge"><title>19&#45;&gt;18</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="889.602,-398.4 879.24,-396.19 885.962,-404.379 889.602,-398.4"/>
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<!-- 19&#45;&gt;25 -->
<g id="edge45" class="edge"><title>19&#45;&gt;25</title>
<path fill="none" stroke="grey" stroke-width="2" d="M967.332,-431.807C967.882,-411.847 965.54,-379.215 947,-360 941.799,-354.609 861.991,-335.541 802.055,-321.821"/>
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<!-- 20&#45;&gt;9 -->
<g id="edge23" class="edge"><title>20&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M846.292,-215.697C844.639,-207.983 842.653,-198.712 840.81,-190.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="844.183,-189.149 838.665,-180.104 837.338,-190.616 844.183,-189.149"/>
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<!-- 21 -->
<g id="node22" class="node"><title>21</title>
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<text text-anchor="middle" x="1014" y="-303.5" font-family="sans" font-size="10.00">generate_alfa_index</text>
</g>
<!-- 21&#45;&gt;9 -->
<g id="edge24" class="edge"><title>21&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M998.839,-287.668C981.776,-268.746 952.678,-238.186 924,-216 907.558,-203.28 887.819,-191.241 871.112,-181.862"/>
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<!-- 22 -->
<g id="node23" class="node"><title>22</title>
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<text text-anchor="middle" x="344" y="-591.5" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
</g>
<!-- 22&#45;&gt;11 -->
<g id="edge26" class="edge"><title>22&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M342.764,-575.697C342.213,-567.983 341.551,-558.712 340.937,-550.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="344.425,-549.83 340.222,-540.104 337.443,-550.328 344.425,-549.83"/>
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<!-- 23 -->
<g id="node24" class="node"><title>23</title>
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<text text-anchor="middle" x="195" y="-591.5" font-family="sans" font-size="10.00">extract_transcriptome</text>
</g>
<!-- 23&#45;&gt;12 -->
<g id="edge27" class="edge"><title>23&#45;&gt;12</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="198.5,-550.104 195,-540.104 191.5,-550.104 198.5,-550.104"/>
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<!-- 26 -->
<g id="node27" class="node"><title>26</title>
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<text text-anchor="middle" x="480" y="-519.5" font-family="sans" font-size="10.00">create_index_salmon</text>
</g>
<!-- 23&#45;&gt;26 -->
<g id="edge46" class="edge"><title>23&#45;&gt;26</title>
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<!-- 24 -->
<g id="node25" class="node"><title>24</title>
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<text text-anchor="middle" x="613" y="-591.5" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
</g>
<!-- 24&#45;&gt;13 -->
<g id="edge28" class="edge"><title>24&#45;&gt;13</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="616.5,-550.104 613,-540.104 609.5,-550.104 616.5,-550.104"/>
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<!-- 25&#45;&gt;14 -->
<g id="edge29" class="edge"><title>25&#45;&gt;14</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="597.749,-252.161 587.155,-252.111 595.406,-258.757 597.749,-252.161"/>
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<!-- 26&#45;&gt;15 -->
<g id="edge30" class="edge"><title>26&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M464.18,-503.697C456.43,-495.22 446.961,-484.864 438.476,-475.583"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="440.969,-473.123 431.638,-468.104 435.803,-477.846 440.969,-473.123"/>
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<!-- 26&#45;&gt;16 -->
<g id="edge32" class="edge"><title>26&#45;&gt;16</title>
<path fill="none" stroke="grey" stroke-width="2" d="M498.045,-503.697C507.062,-495.05 518.118,-484.449 527.943,-475.027"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="530.367,-477.552 535.163,-468.104 525.522,-472.499 530.367,-477.552"/>
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<!-- 27 -->
<g id="node28" class="node"><title>27</title>
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<text text-anchor="middle" x="966" y="-519.5" font-family="sans" font-size="10.00">create_index_star</text>
</g>
<!-- 27&#45;&gt;17 -->
<g id="edge34" class="edge"><title>27&#45;&gt;17</title>
<path fill="none" stroke="grey" stroke-width="2" d="M935.911,-503.876C919.68,-494.639 899.458,-483.131 882.029,-473.212"/>
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<!-- 27&#45;&gt;19 -->
<g id="edge38" class="edge"><title>27&#45;&gt;19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M966,-503.697C966,-495.983 966,-486.712 966,-478.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="969.5,-478.104 966,-468.104 962.5,-478.104 969.5,-478.104"/>
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<!-- 27&#45;&gt;21 -->
<g id="edge41" class="edge"><title>27&#45;&gt;21</title>
<path fill="none" stroke="grey" stroke-width="2" d="M993.34,-503.775C1005.11,-494.718 1017.62,-482.478 1024,-468 1043.27,-424.297 1032.42,-367.371 1023.04,-334.235"/>
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<!-- 28 -->
<g id="node29" class="node"><title>28</title>
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<text text-anchor="middle" x="635" y="-375.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
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<!-- 28&#45;&gt;25 -->
<g id="edge43" class="edge"><title>28&#45;&gt;25</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="704.972,-332.763 711.198,-324.19 700.985,-327.009 704.972,-332.763"/>
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