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<!-- Title: snakemake_dag Pages: 1 -->
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<!-- 0 -->
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<title>0</title>
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<text text-anchor="middle" x="944.5" y="-15.5" font-family="sans" font-size="10.00" fill="#000000">finish</text>
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<title>1</title>
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<text text-anchor="middle" x="162.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">pe_fastqc</text>
<text text-anchor="middle" x="162.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<title>1->0</title>
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<title>2</title>
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<text text-anchor="middle" x="511.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">fastqc</text>
<text text-anchor="middle" x="511.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<title>2->0</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M619.9262,-71.9707C713.8941,-56.3456 844.3945,-34.6457 907.4564,-24.1597"/>
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<title>3</title>
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<text text-anchor="middle" x="857.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_quantification_salmon</text>
<g id="edge3" class="edge">
<title>3->0</title>
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<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
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<text text-anchor="middle" x="1036.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_genes_tpm</text>
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<!-- 3->9 -->
<g id="edge23" class="edge">
<title>3->9</title>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
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<text text-anchor="middle" x="852.5" y="-87.5" font-family="sans" font-size="10.00" fill="#000000">salmon_quantmerge_tr_tpm</text>
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<!-- 3->10 -->
<g id="edge25" class="edge">
<title>3->10</title>
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<g id="node5" class="node">
<title>4</title>
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<title>4->0</title>
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<!-- 4->9 -->
<g id="edge24" class="edge">
<title>4->9</title>
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<!-- 4->10 -->
<g id="edge26" class="edge">
<title>4->10</title>
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<title>5</title>
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<text text-anchor="middle" x="708.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">pe_genome_quantification_kallisto</text>
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<!-- 5->0 -->
<g id="edge5" class="edge">
<title>5->0</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M708.2829,-218.3577C708.9002,-184.6935 715.1754,-112.3246 755.5,-72 776.8453,-50.6547 858.9524,-33.0222 907.6447,-24.165"/>
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<title>6</title>
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<text text-anchor="middle" x="1166.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">genome_quantification_kallisto</text>
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<!-- 6->0 -->
<g id="edge6" class="edge">
<title>6->0</title>
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<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
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<text text-anchor="middle" x="1325.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
<text text-anchor="middle" x="1325.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: paired_end</text>
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<!-- 7->0 -->
<g id="edge7" class="edge">
<title>7->0</title>
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<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
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<text text-anchor="middle" x="1530.5" y="-93" font-family="sans" font-size="10.00" fill="#000000">calculate_TIN_scores</text>
<text text-anchor="middle" x="1530.5" y="-82" font-family="sans" font-size="10.00" fill="#000000">seqmode: single_end</text>
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<!-- 8->0 -->
<g id="edge8" class="edge">
<title>8->0</title>
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<!-- 9->0 -->
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<title>9->0</title>
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<!-- 10->0 -->
<g id="edge10" class="edge">
<title>10->0</title>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
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<text text-anchor="middle" x="862.5" y="-311" font-family="sans" font-size="10.00" fill="#000000">pe_remove_polya_cutadapt</text>
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<!-- 11->3 -->
<g id="edge11" class="edge">
<title>11->3</title>
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<!-- 11->5 -->
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<title>11->5</title>
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<!-- 20 -->
<g id="node21" class="node">
<title>20</title>
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<text text-anchor="middle" x="1332.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">pe_map_genome_star</text>
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<!-- 11->20 -->
<g id="edge32" class="edge">
<title>11->20</title>
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<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
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<text text-anchor="middle" x="955.5" y="-245" font-family="sans" font-size="10.00" fill="#000000">create_index_salmon</text>
<text text-anchor="middle" x="955.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">kmer: 31</text>
<text text-anchor="middle" x="955.5" y="-223" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
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<!-- 12->3 -->
<g id="edge12" class="edge">
<title>12->3</title>
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<!-- 12->4 -->
<g id="edge14" class="edge">
<title>12->4</title>
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<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
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<text text-anchor="middle" x="1171.5" y="-311" font-family="sans" font-size="10.00" fill="#000000">remove_polya_cutadapt</text>
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<!-- 13->4 -->
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<title>13->4</title>
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<!-- 13->6 -->
<g id="edge17" class="edge">
<title>13->6</title>
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<!-- 21 -->
<g id="node22" class="node">
<title>21</title>
<path fill="none" stroke="#56d8b1" stroke-width="2" d="M1508,-254.5C1508,-254.5 1425,-254.5 1425,-254.5 1419,-254.5 1413,-248.5 1413,-242.5 1413,-242.5 1413,-230.5 1413,-230.5 1413,-224.5 1419,-218.5 1425,-218.5 1425,-218.5 1508,-218.5 1508,-218.5 1514,-218.5 1520,-224.5 1520,-230.5 1520,-230.5 1520,-242.5 1520,-242.5 1520,-248.5 1514,-254.5 1508,-254.5"/>
<text text-anchor="middle" x="1466.5" y="-234" font-family="sans" font-size="10.00" fill="#000000">map_genome_star</text>
</g>
<!-- 13->21 -->
<g id="edge34" class="edge">
<title>13->21</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1238.6681,-298.7385C1283.048,-288.6322 1342.6532,-274.3904 1403.107,-257.3127"/>
<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1404.1559,-260.6532 1412.8145,-254.5476 1402.2382,-253.921 1404.1559,-260.6532"/>
</g>
<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
<path fill="none" stroke="#59d856" stroke-width="2" d="M756,-331.5C756,-331.5 641,-331.5 641,-331.5 635,-331.5 629,-325.5 629,-319.5 629,-319.5 629,-307.5 629,-307.5 629,-301.5 635,-295.5 641,-295.5 641,-295.5 756,-295.5 756,-295.5 762,-295.5 768,-301.5 768,-307.5 768,-307.5 768,-319.5 768,-319.5 768,-325.5 762,-331.5 756,-331.5"/>
<text text-anchor="middle" x="698.5" y="-316.5" font-family="sans" font-size="10.00" fill="#000000">create_index_kallisto</text>
<text text-anchor="middle" x="698.5" y="-305.5" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
</g>
<!-- 14->5 -->
<g id="edge16" class="edge">
<title>14->5</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M700.8699,-295.2521C702.053,-286.1422 703.5107,-274.9174 704.834,-264.7282"/>
<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="708.33,-264.9845 706.1472,-254.6169 701.3883,-264.0829 708.33,-264.9845"/>
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<!-- 14->6 -->
<g id="edge18" class="edge">
<title>14->6</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M766.0419,-295.4294C769.9084,-294.5646 773.7479,-293.7471 777.5,-293 890.6171,-270.478 920.4001,-273.8505 1034.5,-257 1046.448,-255.2355 1058.9976,-253.3405 1071.4094,-251.4412"/>
<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1071.9669,-254.8967 1081.3198,-249.9194 1070.9044,-247.9778 1071.9669,-254.8967"/>
</g>
<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
<path fill="none" stroke="#d86e56" stroke-width="2" d="M1420,-180C1420,-180 1231,-180 1231,-180 1225,-180 1219,-174 1219,-168 1219,-168 1219,-156 1219,-156 1219,-150 1225,-144 1231,-144 1231,-144 1420,-144 1420,-144 1426,-144 1432,-150 1432,-156 1432,-156 1432,-168 1432,-168 1432,-174 1426,-180 1420,-180"/>
<text text-anchor="middle" x="1325.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">pe_index_genomic_alignment_samtools</text>
</g>
<!-- 15->7 -->
<g id="edge19" class="edge">
<title>15->7</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1325.5,-143.8314C1325.5,-136.131 1325.5,-126.9743 1325.5,-118.4166"/>
<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1329.0001,-118.4132 1325.5,-108.4133 1322.0001,-118.4133 1329.0001,-118.4132"/>
</g>
<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
<path fill="none" stroke="#569ad8" stroke-width="2" d="M1598.5,-180C1598.5,-180 1462.5,-180 1462.5,-180 1456.5,-180 1450.5,-174 1450.5,-168 1450.5,-168 1450.5,-156 1450.5,-156 1450.5,-150 1456.5,-144 1462.5,-144 1462.5,-144 1598.5,-144 1598.5,-144 1604.5,-144 1610.5,-150 1610.5,-156 1610.5,-156 1610.5,-168 1610.5,-168 1610.5,-174 1604.5,-180 1598.5,-180"/>
<text text-anchor="middle" x="1530.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">extract_transcripts_as_bed12</text>
</g>
<!-- 16->7 -->
<g id="edge20" class="edge">
<title>16->7</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1479.0345,-143.9243C1451.0098,-134.0815 1416.1516,-121.8386 1386.736,-111.5073"/>
<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1387.5816,-108.0947 1376.9867,-108.0831 1385.2619,-114.6992 1387.5816,-108.0947"/>
</g>
<!-- 16->8 -->
<g id="edge22" class="edge">
<title>16->8</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1530.5,-143.8314C1530.5,-136.131 1530.5,-126.9743 1530.5,-118.4166"/>
<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1534.0001,-118.4132 1530.5,-108.4133 1527.0001,-118.4133 1534.0001,-118.4132"/>
</g>
<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
<path fill="none" stroke="#56d8c9" stroke-width="2" d="M1812.5,-180C1812.5,-180 1640.5,-180 1640.5,-180 1634.5,-180 1628.5,-174 1628.5,-168 1628.5,-168 1628.5,-156 1628.5,-156 1628.5,-150 1634.5,-144 1640.5,-144 1640.5,-144 1812.5,-144 1812.5,-144 1818.5,-144 1824.5,-150 1824.5,-156 1824.5,-156 1824.5,-168 1824.5,-168 1824.5,-174 1818.5,-180 1812.5,-180"/>
<text text-anchor="middle" x="1726.5" y="-159.5" font-family="sans" font-size="10.00" fill="#000000">index_genomic_alignment_samtools</text>
</g>
<!-- 17->8 -->
<g id="edge21" class="edge">
<title>17->8</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1677.2939,-143.9243C1650.6161,-134.1243 1617.4614,-121.945 1589.4148,-111.6422"/>
<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="1590.3199,-108.246 1579.7263,-108.0831 1587.9062,-114.8167 1590.3199,-108.246"/>
</g>
<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
<path fill="none" stroke="#d8b456" stroke-width="2" d="M993,-406C993,-406 692,-406 692,-406 686,-406 680,-400 680,-394 680,-394 680,-382 680,-382 680,-376 686,-370 692,-370 692,-370 993,-370 993,-370 999,-370 1005,-376 1005,-382 1005,-382 1005,-394 1005,-394 1005,-400 999,-406 993,-406"/>
<text text-anchor="middle" x="842.5" y="-391" font-family="sans" font-size="10.00" fill="#000000">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="842.5" y="-380" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
</g>
<!-- 18->11 -->
<g id="edge27" class="edge">
<title>18->11</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M847.3414,-369.9656C849.6337,-361.427 852.424,-351.0333 854.9827,-341.502"/>
<polygon fill="#c0c0c0" stroke="#c0c0c0" stroke-width="2" points="858.4213,-342.192 857.6338,-331.6265 851.6607,-340.3771 858.4213,-342.192"/>
</g>
<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
<path fill="none" stroke="#70d856" stroke-width="2" d="M1348,-406C1348,-406 1035,-406 1035,-406 1029,-406 1023,-400 1023,-394 1023,-394 1023,-382 1023,-382 1023,-376 1029,-370 1035,-370 1035,-370 1348,-370 1348,-370 1354,-370 1360,-376 1360,-382 1360,-382 1360,-394 1360,-394 1360,-400 1354,-406 1348,-406"/>
<text text-anchor="middle" x="1191.5" y="-391" font-family="sans" font-size="10.00" fill="#000000">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="1191.5" y="-380" font-family="sans" font-size="10.00" fill="#000000">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<!-- 19->13 -->
<g id="edge28" class="edge">
<title>19->13</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1186.6586,-369.9656C1184.3663,-361.427 1181.576,-351.0333 1179.0173,-341.502"/>
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<!-- 20->15 -->
<g id="edge29" class="edge">
<title>20->15</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1330.8055,-218.4656C1330.0117,-210.0178 1329.0474,-199.7542 1328.1597,-190.3064"/>
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<!-- 21->17 -->
<g id="edge30" class="edge">
<title>21->17</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1520.0569,-221.1539C1558.6725,-210.089 1611.2447,-195.0251 1653.6717,-182.8681"/>
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<!-- 22 -->
<g id="node23" class="node">
<title>22</title>
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<text text-anchor="middle" x="1399.5" y="-322" font-family="sans" font-size="10.00" fill="#000000">create_index_star</text>
<text text-anchor="middle" x="1399.5" y="-311" font-family="sans" font-size="10.00" fill="#000000">index_size: 75</text>
<text text-anchor="middle" x="1399.5" y="-300" font-family="sans" font-size="10.00" fill="#000000">organism: homo_sapiens</text>
</g>
<!-- 22->20 -->
<g id="edge31" class="edge">
<title>22->20</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1381.5452,-292.8654C1373.3483,-283.445 1363.5558,-272.191 1354.8841,-262.225"/>
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<!-- 22->21 -->
<g id="edge33" class="edge">
<title>22->21</title>
<path fill="none" stroke="#c0c0c0" stroke-width="2" d="M1417.4548,-292.8654C1425.6517,-283.445 1435.4442,-272.191 1444.1159,-262.225"/>
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