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<!-- Title: snakemake_dag Pages: 1 -->
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<g id="node1" class="node"><title>0</title>
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<text text-anchor="middle" x="1035" y="-15.5" font-family="sans" font-size="10.00">finish</text>
<g id="node2" class="node"><title>1</title>
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<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>
<g id="edge1" class="edge"><title>1->0</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>
<g id="edge2" class="edge"><title>2->0</title>
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<text text-anchor="middle" x="988" y="-159.5" font-family="sans" font-size="10.00">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="1286" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="1286" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<!-- 3->9 -->
<g id="edge25" class="edge"><title>3->9</title>
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<!-- 10 -->
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<text text-anchor="middle" x="781" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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<!-- 3->10 -->
<g id="edge27" class="edge"><title>3->10</title>
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<!-- 11 -->
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<text text-anchor="middle" x="949" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: tpm</text>
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<!-- 3->11 -->
<g id="edge29" class="edge"><title>3->11</title>
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<!-- 12 -->
<g id="node13" class="node"><title>12</title>
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<text text-anchor="middle" x="1122" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
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<!-- 3->12 -->
<g id="edge31" class="edge"><title>3->12</title>
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<text text-anchor="middle" x="1125" y="-159.5" font-family="sans" font-size="10.00">quantification_salmon</text>
<g id="edge4" class="edge"><title>4->0</title>
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<!-- 4->9 -->
<g id="edge26" class="edge"><title>4->9</title>
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<!-- 4->10 -->
<g id="edge28" class="edge"><title>4->10</title>
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<!-- 4->11 -->
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<!-- 4->12 -->
<g id="edge32" class="edge"><title>4->12</title>
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<text text-anchor="middle" x="854" y="-234" font-family="sans" font-size="10.00">pe_genome_quantification_kallisto</text>
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<!-- 5->0 -->
<g id="edge5" class="edge"><title>5->0</title>
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<text text-anchor="middle" x="1320" y="-234" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
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<!-- 6->0 -->
<g id="edge6" class="edge"><title>6->0</title>
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<!-- 7 -->
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<text text-anchor="middle" x="1504" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="1504" y="-82" font-family="sans" font-size="10.00">seqmode: paired_end</text>
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<!-- 7->0 -->
<g id="edge7" class="edge"><title>7->0</title>
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<!-- 8 -->
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<text text-anchor="middle" x="1689" y="-93" font-family="sans" font-size="10.00">calculate_TIN_scores</text>
<text text-anchor="middle" x="1689" y="-82" font-family="sans" font-size="10.00">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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<!-- 10->0 -->
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<!-- 13 -->
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<text text-anchor="middle" x="1003" y="-311" font-family="sans" font-size="10.00">pe_remove_polya_cutadapt</text>
<!-- 13->3 -->
<g id="edge13" class="edge"><title>13->3</title>
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<!-- 13->5 -->
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<!-- 22 -->
<g id="node23" class="node"><title>22</title>
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<text text-anchor="middle" x="1496" y="-234" font-family="sans" font-size="10.00">pe_map_genome_star</text>
<!-- 13->22 -->
<g id="edge38" class="edge"><title>13->22</title>
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<!-- 14 -->
<g id="node15" class="node"><title>14</title>
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<text text-anchor="middle" x="1103" y="-245" font-family="sans" font-size="10.00">create_index_salmon</text>
<text text-anchor="middle" x="1103" y="-234" font-family="sans" font-size="10.00">kmer: 31</text>
<text text-anchor="middle" x="1103" y="-223" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 14->3 -->
<g id="edge14" class="edge"><title>14->3</title>
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<!-- 14->4 -->
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<!-- 15 -->
<g id="node16" class="node"><title>15</title>
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<text text-anchor="middle" x="1320" y="-311" font-family="sans" font-size="10.00">remove_polya_cutadapt</text>
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<!-- 15->4 -->
<g id="edge15" class="edge"><title>15->4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1292.2,-295.305C1275.56,-284.728 1254.18,-270.629 1236,-257 1205.95,-234.472 1173.35,-206.391 1151.3,-186.814"/>
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<!-- 15->6 -->
<g id="edge19" class="edge"><title>15->6</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1323.5,-264.711 1320,-254.711 1316.5,-264.711 1323.5,-264.711"/>
</g>
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<g id="node24" class="node"><title>23</title>
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<text text-anchor="middle" x="1619" y="-234" font-family="sans" font-size="10.00">map_genome_star</text>
</g>
<!-- 15->23 -->
<g id="edge40" class="edge"><title>15->23</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1561.62,-260.631 1570.29,-254.538 1559.71,-253.896 1561.62,-260.631"/>
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<!-- 16 -->
<g id="node17" class="node"><title>16</title>
<path fill="none" stroke="#d8b456" stroke-width="2" d="M904.5,-331.5C904.5,-331.5 803.5,-331.5 803.5,-331.5 797.5,-331.5 791.5,-325.5 791.5,-319.5 791.5,-319.5 791.5,-307.5 791.5,-307.5 791.5,-301.5 797.5,-295.5 803.5,-295.5 803.5,-295.5 904.5,-295.5 904.5,-295.5 910.5,-295.5 916.5,-301.5 916.5,-307.5 916.5,-307.5 916.5,-319.5 916.5,-319.5 916.5,-325.5 910.5,-331.5 904.5,-331.5"/>
<text text-anchor="middle" x="854" y="-316.5" font-family="sans" font-size="10.00">create_index_kallisto</text>
<text text-anchor="middle" x="854" y="-305.5" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 16->5 -->
<g id="edge18" class="edge"><title>16->5</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="857.5,-264.711 854,-254.711 850.5,-264.711 857.5,-264.711"/>
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<!-- 16->6 -->
<g id="edge20" class="edge"><title>16->6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M914.759,-295.473C918.551,-294.588 922.321,-293.754 926,-293 955.541,-286.944 1128.09,-263.327 1234.82,-248.924"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1235.49,-252.365 1244.93,-247.56 1234.56,-245.428 1235.49,-252.365"/>
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<!-- 17 -->
<g id="node18" class="node"><title>17</title>
<path fill="none" stroke="#56d86b" stroke-width="2" d="M1586,-180C1586,-180 1420,-180 1420,-180 1414,-180 1408,-174 1408,-168 1408,-168 1408,-156 1408,-156 1408,-150 1414,-144 1420,-144 1420,-144 1586,-144 1586,-144 1592,-144 1598,-150 1598,-156 1598,-156 1598,-168 1598,-168 1598,-174 1592,-180 1586,-180"/>
<text text-anchor="middle" x="1503" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
<!-- 17->7 -->
<g id="edge21" class="edge"><title>17->7</title>
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<!-- 18 -->
<g id="node19" class="node"><title>18</title>
<path fill="none" stroke="#56b1d8" stroke-width="2" d="M1749.5,-180C1749.5,-180 1628.5,-180 1628.5,-180 1622.5,-180 1616.5,-174 1616.5,-168 1616.5,-168 1616.5,-156 1616.5,-156 1616.5,-150 1622.5,-144 1628.5,-144 1628.5,-144 1749.5,-144 1749.5,-144 1755.5,-144 1761.5,-150 1761.5,-156 1761.5,-156 1761.5,-168 1761.5,-168 1761.5,-174 1755.5,-180 1749.5,-180"/>
<text text-anchor="middle" x="1689" y="-159.5" font-family="sans" font-size="10.00">extract_transcripts_as_bed12</text>
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<!-- 18->7 -->
<g id="edge22" class="edge"><title>18->7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1643.74,-143.876C1618,-134.137 1585.59,-121.872 1558.46,-111.608"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="1559.7,-108.334 1549.11,-108.068 1557.22,-114.881 1559.7,-108.334"/>
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<!-- 18->8 -->
<g id="edge24" class="edge"><title>18->8</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="1692.5,-118.104 1689,-108.104 1685.5,-118.104 1692.5,-118.104"/>
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<!-- 19 -->
<g id="node20" class="node"><title>19</title>
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<text text-anchor="middle" x="1867" y="-159.5" font-family="sans" font-size="10.00">index_genomic_alignment_samtools</text>
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<!-- 19->8 -->
<g id="edge23" class="edge"><title>19->8</title>
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<!-- 20 -->
<g id="node21" class="node"><title>20</title>
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<text text-anchor="middle" x="1003" y="-391" font-family="sans" font-size="10.00">pe_remove_adapters_cutadapt</text>
<text text-anchor="middle" x="1003" y="-380" font-family="sans" font-size="10.00">sample: synthetic_10_reads_paired_synthetic_10_reads_paired</text>
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<!-- 20->13 -->
<g id="edge33" class="edge"><title>20->13</title>
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<!-- 21 -->
<g id="node22" class="node"><title>21</title>
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<text text-anchor="middle" x="1320" y="-391" font-family="sans" font-size="10.00">remove_adapters_cutadapt</text>
<text text-anchor="middle" x="1320" y="-380" font-family="sans" font-size="10.00">sample: synthetic_10_reads_mate_1_synthetic_10_reads_mate_1</text>
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<!-- 21->15 -->
<g id="edge34" class="edge"><title>21->15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M1320,-369.819C1320,-361.422 1320,-351.116 1320,-341.686"/>
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<!-- 22->17 -->
<g id="edge35" class="edge"><title>22->17</title>
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<!-- 23->19 -->
<g id="edge36" class="edge"><title>23->19</title>
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<!-- 24 -->
<g id="node25" class="node"><title>24</title>
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<text text-anchor="middle" x="1557" y="-322" font-family="sans" font-size="10.00">create_index_star</text>
<text text-anchor="middle" x="1557" y="-311" font-family="sans" font-size="10.00">index_size: 75</text>
<text text-anchor="middle" x="1557" y="-300" font-family="sans" font-size="10.00">organism: homo_sapiens</text>
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<!-- 24->22 -->
<g id="edge37" class="edge"><title>24->22</title>
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<!-- 24->23 -->
<g id="edge39" class="edge"><title>24->23</title>
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