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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)
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<!-- Title: snakemake_dag Pages: 1 -->
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<title>snakemake_dag</title>
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<!-- 0 -->
<g id="node1" class="node"><title>0</title>
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<text text-anchor="middle" x="699" y="-15.5" font-family="sans" font-size="10.00">finish</text>
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<!-- 1 -->
<g id="node2" class="node"><title>1</title>
<path fill="none" stroke="#d8a456" stroke-width="2" d="M280,-108C280,-108 12,-108 12,-108 6,-108 0,-102 0,-96 0,-96 0,-84 0,-84 0,-78 6,-72 12,-72 12,-72 280,-72 280,-72 286,-72 292,-78 292,-84 292,-84 292,-96 292,-96 292,-102 286,-108 280,-108"/>
<text text-anchor="middle" x="146" y="-93" font-family="sans" font-size="10.00">pe_fastqc</text>
<text text-anchor="middle" x="146" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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</g>
<!-- 1&#45;&gt;0 -->
<g id="edge1" class="edge"><title>1&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M280.572,-71.9656C406.068,-56.08 585.083,-33.4199 661.788,-23.7104"/>
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</g>
<!-- 2 -->
<g id="node3" class="node"><title>2</title>
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<text text-anchor="middle" x="462" y="-93" font-family="sans" font-size="10.00">fastqc</text>
<text text-anchor="middle" x="462" y="-82" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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</g>
<!-- 2&#45;&gt;0 -->
<g id="edge2" class="edge"><title>2&#45;&gt;0</title>
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</g>
<!-- 3 -->
<g id="node4" class="node"><title>3</title>
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<text text-anchor="middle" x="462" y="-231.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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</g>
<!-- 3&#45;&gt;0 -->
<g id="edge3" class="edge"><title>3&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M487.264,-215.826C520.088,-192.982 578.459,-150.513 623,-108 643.903,-88.0485 665.037,-62.797 679.694,-44.2918"/>
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</g>
<!-- 4 -->
<g id="node5" class="node"><title>4</title>
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<text text-anchor="middle" x="599" y="-231.5" font-family="sans" font-size="10.00">quantification_salmon</text>
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<!-- 4&#45;&gt;0 -->
<g id="edge4" class="edge"><title>4&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M623.094,-215.785C634.597,-206.411 647.644,-193.897 656,-180 681.56,-137.492 692.17,-79.7097 696.391,-46.1773"/>
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</g>
<!-- 5 -->
<g id="node6" class="node"><title>5</title>
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<text text-anchor="middle" x="756" y="-231.5" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
<g id="edge5" class="edge"><title>5&#45;&gt;0</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="709.546,-44.9947 703.59,-36.2325 702.782,-46.7964 709.546,-44.9947"/>
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</g>
<!-- 6 -->
<g id="node7" class="node"><title>6</title>
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<text text-anchor="middle" x="932" y="-231.5" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
<g id="edge6" class="edge"><title>6&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M863.1,-215.882C827.305,-205.814 788.309,-192.618 775,-180 737.506,-144.455 755.302,-118.111 732,-72 727.356,-62.8095 721.614,-53.1415 716.229,-44.6159"/>
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<g id="node8" class="node"><title>7</title>
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<text text-anchor="middle" x="879" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="879" y="-82" font-family="sans" font-size="10.00">seqmode: paired_end</text>
<g id="edge7" class="edge"><title>7&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M834.967,-71.8761C804.523,-60.0365 764.485,-44.4665 735.753,-33.293"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="736.685,-29.8999 726.096,-29.5374 734.148,-36.424 736.685,-29.8999"/>
<g id="node9" class="node"><title>8</title>
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<text text-anchor="middle" x="1065" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="1065" y="-82" font-family="sans" font-size="10.00">seqmode: single_end</text>
<g id="edge8" class="edge"><title>8&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1008.61,-78.2159C933.016,-63.7572 800.875,-38.4843 736.452,-26.1629"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="736.823,-22.6705 726.343,-24.2296 735.508,-29.5459 736.823,-22.6705"/>
<g id="node10" class="node"><title>9</title>
<path fill="none" stroke="#bed856" stroke-width="2" d="M726,-326.5C726,-326.5 614,-326.5 614,-326.5 608,-326.5 602,-320.5 602,-314.5 602,-314.5 602,-302.5 602,-302.5 602,-296.5 608,-290.5 614,-290.5 614,-290.5 726,-290.5 726,-290.5 732,-290.5 738,-296.5 738,-302.5 738,-302.5 738,-314.5 738,-314.5 738,-320.5 732,-326.5 726,-326.5"/>
<text text-anchor="middle" x="670" y="-306" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
<g id="edge9" class="edge"><title>9&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M620.97,-290.41C590.929,-279.939 552.3,-266.475 520.644,-255.441"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="521.655,-252.087 511.061,-252.1 519.351,-258.697 521.655,-252.087"/>
</g>
<!-- 9&#45;&gt;5 -->
<g id="edge13" class="edge"><title>9&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M690.381,-290.319C701.627,-280.838 715.758,-268.925 728.024,-258.585"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="730.376,-261.18 735.765,-252.058 725.864,-255.828 730.376,-261.18"/>
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<!-- 18 -->
<g id="node19" class="node"><title>18</title>
<path fill="none" stroke="#70d856" stroke-width="2" d="M1126.5,-252C1126.5,-252 1037.5,-252 1037.5,-252 1031.5,-252 1025.5,-246 1025.5,-240 1025.5,-240 1025.5,-228 1025.5,-228 1025.5,-222 1031.5,-216 1037.5,-216 1037.5,-216 1126.5,-216 1126.5,-216 1132.5,-216 1138.5,-222 1138.5,-228 1138.5,-228 1138.5,-240 1138.5,-240 1138.5,-246 1132.5,-252 1126.5,-252"/>
<text text-anchor="middle" x="1082" y="-231.5" font-family="sans" font-size="10.00">pe_map_genome_star</text>
</g>
<!-- 9&#45;&gt;18 -->
<g id="edge26" class="edge"><title>9&#45;&gt;18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M738.35,-290.717C742.959,-289.749 747.541,-288.832 752,-288 865.226,-266.87 898.018,-274.364 1015.13,-252.03"/>
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<g id="node11" class="node"><title>10</title>
<path fill="none" stroke="#56d8a2" stroke-width="2" d="M541.5,-329C541.5,-329 440.5,-329 440.5,-329 434.5,-329 428.5,-323 428.5,-317 428.5,-317 428.5,-300 428.5,-300 428.5,-294 434.5,-288 440.5,-288 440.5,-288 541.5,-288 541.5,-288 547.5,-288 553.5,-294 553.5,-300 553.5,-300 553.5,-317 553.5,-317 553.5,-323 547.5,-329 541.5,-329"/>
<text text-anchor="middle" x="491" y="-317" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="491" y="-306" font-family="sans" font-size="10.00">kmer: 31</text>
<text text-anchor="middle" x="491" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
</g>
<!-- 10&#45;&gt;3 -->
<g id="edge10" class="edge"><title>10&#45;&gt;3</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="475.891,-260.304 468.928,-252.319 469.392,-262.904 475.891,-260.304"/>
<g id="edge12" class="edge"><title>10&#45;&gt;4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M520.226,-287.88C533.987,-278.643 550.489,-267.565 564.825,-257.941"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="567.076,-260.646 573.428,-252.166 563.174,-254.834 567.076,-260.646"/>
<g id="node12" class="node"><title>11</title>
<path fill="none" stroke="#d86e56" stroke-width="2" d="M1015,-326.5C1015,-326.5 919,-326.5 919,-326.5 913,-326.5 907,-320.5 907,-314.5 907,-314.5 907,-302.5 907,-302.5 907,-296.5 913,-290.5 919,-290.5 919,-290.5 1015,-290.5 1015,-290.5 1021,-290.5 1027,-296.5 1027,-302.5 1027,-302.5 1027,-314.5 1027,-314.5 1027,-320.5 1021,-326.5 1015,-326.5"/>
<text text-anchor="middle" x="967" y="-306" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
</g>
<!-- 11&#45;&gt;4 -->
<g id="edge11" class="edge"><title>11&#45;&gt;4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M906.62,-290.63C902.698,-289.695 898.8,-288.808 895,-288 796.444,-267.04 767.467,-272.788 664.451,-251.962"/>
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<!-- 11&#45;&gt;6 -->
<g id="edge15" class="edge"><title>11&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M958.705,-290.319C954.521,-281.651 949.355,-270.949 944.685,-261.276"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="947.734,-259.542 940.235,-252.058 941.431,-262.585 947.734,-259.542"/>
</g>
<!-- 19 -->
<g id="node20" class="node"><title>19</title>
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<text text-anchor="middle" x="1205" y="-231.5" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 11&#45;&gt;19 -->
<g id="edge28" class="edge"><title>11&#45;&gt;19</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1023.1,-290.41C1060.19,-279.112 1108.72,-264.329 1146.32,-252.874"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1147.58,-256.15 1156.13,-249.888 1145.54,-249.454 1147.58,-256.15"/>
<g id="node13" class="node"><title>12</title>
<path fill="none" stroke="#56d8d8" stroke-width="2" d="M873.5,-326.5C873.5,-326.5 772.5,-326.5 772.5,-326.5 766.5,-326.5 760.5,-320.5 760.5,-314.5 760.5,-314.5 760.5,-302.5 760.5,-302.5 760.5,-296.5 766.5,-290.5 772.5,-290.5 772.5,-290.5 873.5,-290.5 873.5,-290.5 879.5,-290.5 885.5,-296.5 885.5,-302.5 885.5,-302.5 885.5,-314.5 885.5,-314.5 885.5,-320.5 879.5,-326.5 873.5,-326.5"/>
<text text-anchor="middle" x="823" y="-311.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
<text text-anchor="middle" x="823" y="-300.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
<g id="edge14" class="edge"><title>12&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M807.122,-290.319C798.611,-281.109 787.979,-269.604 778.618,-259.475"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="781.122,-257.027 771.764,-252.058 775.981,-261.778 781.122,-257.027"/>
<g id="edge16" class="edge"><title>12&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M848.831,-290.319C863.492,-280.567 882.022,-268.242 897.868,-257.702"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="899.966,-260.511 906.354,-252.058 896.089,-254.682 899.966,-260.511"/>
<g id="node14" class="node"><title>13</title>
<path fill="none" stroke="#a7d856" stroke-width="2" d="M962,-180C962,-180 796,-180 796,-180 790,-180 784,-174 784,-168 784,-168 784,-156 784,-156 784,-150 790,-144 796,-144 796,-144 962,-144 962,-144 968,-144 974,-150 974,-156 974,-156 974,-168 974,-168 974,-174 968,-180 962,-180"/>
<text text-anchor="middle" x="879" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
</g>
<!-- 13&#45;&gt;7 -->
<g id="edge17" class="edge"><title>13&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M879,-143.697C879,-135.983 879,-126.712 879,-118.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="882.5,-118.104 879,-108.104 875.5,-118.104 882.5,-118.104"/>
<g id="node15" class="node"><title>14</title>
<path fill="none" stroke="#56d873" stroke-width="2" d="M1125.5,-180C1125.5,-180 1004.5,-180 1004.5,-180 998.5,-180 992.5,-174 992.5,-168 992.5,-168 992.5,-156 992.5,-156 992.5,-150 998.5,-144 1004.5,-144 1004.5,-144 1125.5,-144 1125.5,-144 1131.5,-144 1137.5,-150 1137.5,-156 1137.5,-156 1137.5,-168 1137.5,-168 1137.5,-174 1131.5,-180 1125.5,-180"/>
<text text-anchor="middle" x="1065" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
<g id="edge18" class="edge"><title>14&#45;&gt;7</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="934.945,-108.315 924.353,-108.068 932.479,-114.866 934.945,-108.315"/>
<g id="edge20" class="edge"><title>14&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1065,-143.697C1065,-135.983 1065,-126.712 1065,-118.112"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1068.5,-118.104 1065,-108.104 1061.5,-118.104 1068.5,-118.104"/>
<g id="node16" class="node"><title>15</title>
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<text text-anchor="middle" x="1243" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
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<!-- 15&#45;&gt;8 -->
<g id="edge19" class="edge"><title>15&#45;&gt;8</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1199.46,-143.876C1174.8,-134.179 1143.78,-121.98 1117.75,-111.743"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1118.99,-108.471 1108.4,-108.068 1116.43,-114.985 1118.99,-108.471"/>
<g id="node17" class="node"><title>16</title>
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<text text-anchor="middle" x="657" y="-386" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="657" y="-375" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<!-- 16&#45;&gt;9 -->
<g id="edge21" class="edge"><title>16&#45;&gt;9</title>
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<g id="node18" class="node"><title>17</title>
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<text text-anchor="middle" x="973" y="-386" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="973" y="-375" 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="1143" y="-317" font-family="sans" font-size="10.00">create_index_star</text>
<text text-anchor="middle" x="1143" y="-306" font-family="sans" font-size="10.00">index_size: 75</text>
<text text-anchor="middle" x="1143" y="-295" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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Alex Kanitz's avatar
Alex Kanitz committed
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