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<!-- 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="1035" 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>
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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>
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<!-- 1&#45;&gt;0 -->
<g id="edge1" class="edge"><title>1&#45;&gt;0</title>
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<!-- 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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<!-- 2&#45;&gt;0 -->
<g id="edge2" 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="988" y="-159.5" font-family="sans" font-size="10.00">pe_quantification_salmon</text>
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<!-- 3&#45;&gt;0 -->
<g id="edge3" class="edge"><title>3&#45;&gt;0</title>
<path fill="none" stroke="grey" stroke-width="2" d="M924.308,-161.332C821.372,-159.74 636.097,-146.808 700,-72 737.975,-27.5452 918.617,-20.167 997.736,-19.0937"/>
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<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>
<g id="edge25" class="edge"><title>3&#45;&gt;9</title>
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<g id="node11" class="node"><title>10</title>
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<text text-anchor="middle" x="781" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_genes</text>
<text text-anchor="middle" x="781" y="-82" font-family="sans" font-size="10.00">salmon_merge_on: numreads</text>
<g id="edge27" class="edge"><title>3&#45;&gt;10</title>
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<!-- 11 -->
<g id="node12" class="node"><title>11</title>
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<text text-anchor="middle" x="949" y="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
<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&#45;&gt;11 -->
<g id="edge29" class="edge"><title>3&#45;&gt;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="-93" font-family="sans" font-size="10.00">salmon_quantmerge_transcripts</text>
<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&#45;&gt;12 -->
<g id="edge31" class="edge"><title>3&#45;&gt;12</title>
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<!-- 4 -->
<g id="node5" class="node"><title>4</title>
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<text text-anchor="middle" x="1125" y="-159.5" 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="M1180.58,-158.69C1266.45,-153.149 1416.19,-134.476 1363,-72 1326.04,-28.5839 1150.54,-20.6164 1072.53,-19.2392"/>
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<g id="edge26" class="edge"><title>4&#45;&gt;9</title>
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<g id="edge28" class="edge"><title>4&#45;&gt;10</title>
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<!-- 4&#45;&gt;11 -->
<g id="edge30" class="edge"><title>4&#45;&gt;11</title>
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<!-- 4&#45;&gt;12 -->
<g id="edge32" class="edge"><title>4&#45;&gt;12</title>
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<!-- 5 -->
<g id="node6" class="node"><title>5</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>
<g id="edge5" class="edge"><title>5&#45;&gt;0</title>
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<!-- 6 -->
<g id="node7" class="node"><title>6</title>
<path fill="none" stroke="#d89c56" stroke-width="2" d="M1383,-254.5C1383,-254.5 1257,-254.5 1257,-254.5 1251,-254.5 1245,-248.5 1245,-242.5 1245,-242.5 1245,-230.5 1245,-230.5 1245,-224.5 1251,-218.5 1257,-218.5 1257,-218.5 1383,-218.5 1383,-218.5 1389,-218.5 1395,-224.5 1395,-230.5 1395,-230.5 1395,-242.5 1395,-242.5 1395,-248.5 1389,-254.5 1383,-254.5"/>
<text text-anchor="middle" x="1320" y="-234" font-family="sans" font-size="10.00">genome_quantification_kallisto</text>
<g id="edge6" class="edge"><title>6&#45;&gt;0</title>
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<g id="node8" class="node"><title>7</title>
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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>
<g id="edge7" class="edge"><title>7&#45;&gt;0</title>
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<g id="node9" class="node"><title>8</title>
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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>
<g id="edge8" class="edge"><title>8&#45;&gt;0</title>
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<g id="edge9" class="edge"><title>9&#45;&gt;0</title>
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<g id="edge10" class="edge"><title>10&#45;&gt;0</title>
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<!-- 11&#45;&gt;0 -->
<g id="edge11" class="edge"><title>11&#45;&gt;0</title>
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<!-- 12&#45;&gt;0 -->
<g id="edge12" class="edge"><title>12&#45;&gt;0</title>
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<!-- 13 -->
<g id="node14" class="node"><title>13</title>
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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&#45;&gt;3 -->
<g id="edge13" class="edge"><title>13&#45;&gt;3</title>
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<!-- 13&#45;&gt;5 -->
<g id="edge17" class="edge"><title>13&#45;&gt;5</title>
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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&#45;&gt;22 -->
<g id="edge38" class="edge"><title>13&#45;&gt;22</title>
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<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&#45;&gt;3 -->
<g id="edge14" class="edge"><title>14&#45;&gt;3</title>
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<!-- 14&#45;&gt;4 -->
<g id="edge16" class="edge"><title>14&#45;&gt;4</title>
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<g id="node16" class="node"><title>15</title>
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<!-- 15&#45;&gt;4 -->
<g id="edge15" class="edge"><title>15&#45;&gt;4</title>
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<!-- 15&#45;&gt;6 -->
<g id="edge19" class="edge"><title>15&#45;&gt;6</title>
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<!-- 23 -->
<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>
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<!-- 15&#45;&gt;23 -->
<g id="edge40" class="edge"><title>15&#45;&gt;23</title>
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<g id="node17" class="node"><title>16</title>
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<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&#45;&gt;5 -->
<g id="edge18" class="edge"><title>16&#45;&gt;5</title>
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<!-- 16&#45;&gt;6 -->
<g id="edge20" class="edge"><title>16&#45;&gt;6</title>
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<g id="node18" class="node"><title>17</title>
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<text text-anchor="middle" x="1503" y="-159.5" font-family="sans" font-size="10.00">pe_index_genomic_alignment_samtools</text>
<!-- 17&#45;&gt;7 -->
<g id="edge21" class="edge"><title>17&#45;&gt;7</title>
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<g id="node19" class="node"><title>18</title>
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<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&#45;&gt;7 -->
<g id="edge22" class="edge"><title>18&#45;&gt;7</title>
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<!-- 18&#45;&gt;8 -->
<g id="edge24" class="edge"><title>18&#45;&gt;8</title>
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<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>
<!-- 19&#45;&gt;8 -->
<g id="edge23" class="edge"><title>19&#45;&gt;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&#45;&gt;13 -->
<g id="edge33" class="edge"><title>20&#45;&gt;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&#45;&gt;15 -->
<g id="edge34" class="edge"><title>21&#45;&gt;15</title>
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<!-- 22&#45;&gt;17 -->
<g id="edge35" class="edge"><title>22&#45;&gt;17</title>
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<!-- 23&#45;&gt;19 -->
<g id="edge36" class="edge"><title>23&#45;&gt;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&#45;&gt;22 -->
<g id="edge37" class="edge"><title>24&#45;&gt;22</title>
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<!-- 24&#45;&gt;23 -->
<g id="edge39" class="edge"><title>24&#45;&gt;23</title>
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Alex Kanitz's avatar
Alex Kanitz committed
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