/doc/images/gallery/gallery.rna_seq.svg
SVG | 672 lines | 562 code | 0 blank | 110 comment | 0 complexity | 39f59b7614c5538dbf169f79ef74c659 MD5 | raw file
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points="394,-810 272,-810 "/> 312<polyline style="fill:none;stroke:green;" points="394,-810 394,-778 "/> 313<polyline style="fill:none;stroke:green;" points="394,-810 398,-814 "/> 314<text text-anchor="middle" x="335" y="-789.5" style="font-family:Times New Roman;font-size:20.00;">make_replists</text> 315</g> 316<!-- t24->t25 --> 317<g id="edge27" class="edge"><title>t24->t25</title> 318<path style="fill:none;stroke:gray;" d="M334,-778C334,-774 334,-770 334,-766"/> 319<polygon style="fill:gray;stroke:gray;" points="337.5,-766 334,-756 330.5,-766 337.5,-766"/> 320</g> 321<!-- t26 --> 322<g id="node32" class="node"><title>t26</title> 323<polygon style="fill:#90ee90;stroke:green;" points="308.068,-662.774 194,-677.92 79.932,-662.774 80.0385,-638.266 307.961,-638.266 308.068,-662.774"/> 324<polygon style="fill:none;stroke:green;" points="312.066,-666.278 194,-681.955 75.9337,-666.278 76.0727,-634.266 311.927,-634.266 312.066,-666.278"/> 325<text text-anchor="middle" x="194" y="-649.5" style="font-family:Times New Roman;font-size:20.00;">prepare_raw_files</text> 326</g> 327<!-- t25->t26 --> 328<g id="edge29" class="edge"><title>t25->t26</title> 329<path style="fill:none;stroke:gray;" d="M292,-708C277,-700 259,-691 243,-682"/> 330<polygon style="fill:gray;stroke:gray;" points="244.441,-678.797 234,-677 241.042,-684.916 244.441,-678.797"/> 331</g> 332<!-- t34 --> 333<g id="node64" class="node"><title>t34</title> 334<polygon style="fill:#90ee90;stroke:green;" points="665,-674 565,-674 561,-670 561,-638 661,-638 665,-642 665,-674"/> 335<polyline style="fill:none;stroke:green;" points="661,-670 561,-670 "/> 336<polyline style="fill:none;stroke:green;" points="661,-670 661,-638 "/> 337<polyline style="fill:none;stroke:green;" points="661,-670 665,-674 "/> 338<text text-anchor="middle" x="613" y="-649.5" style="font-family:Times New Roman;font-size:20.00;">fill_islands</text> 339</g> 340<!-- t25->t34 --> 341<g id="edge61" class="edge"><title>t25->t34</title> 342<path style="fill:none;stroke:gray;" d="M415,-708C458,-696 511,-682 551,-672"/> 343<polygon style="fill:gray;stroke:gray;" points="551.881,-675.393 561,-670 550.508,-668.529 551.881,-675.393"/> 344</g> 345<!-- t37 --> 346<g id="node70" class="node"><title>t37</title> 347<polygon style="fill:#90ee90;stroke:green;" points="794,-484 582,-484 578,-480 578,-448 790,-448 794,-452 794,-484"/> 348<polyline style="fill:none;stroke:green;" points="790,-480 578,-480 "/> 349<polyline style="fill:none;stroke:green;" points="790,-480 790,-448 "/> 350<polyline style="fill:none;stroke:green;" points="790,-480 794,-484 "/> 351<text text-anchor="middle" x="686" y="-459.5" style="font-family:Times New Roman;font-size:20.00;">Reallocate_Repeat_Ends</text> 352</g> 353<!-- t25->t37 --> 354<g id="edge107" class="edge"><title>t25->t37</title> 355<path style="fill:none;stroke:gray;" d="M353,-708C393,-666 486,-573 577,-514 592,-504 610,-495 626,-488"/> 356<polygon style="fill:gray;stroke:gray;" points="628.015,-490.964 636,-484 625.415,-484.464 628.015,-490.964"/> 357</g> 358<!-- t25->t46 --> 359<g id="edge119" class="edge"><title>t25->t46</title> 360<path style="fill:none;stroke:gray;" d="M331,-708C326,-643 311,-446 311,-282 311,-282 311,-282 311,-216 311,-181 334,-147 354,-125"/> 361<polygon style="fill:gray;stroke:gray;" points="356.404,-127.546 361,-118 351.454,-122.596 356.404,-127.546"/> 362</g> 363<!-- t27 --> 364<g id="node34" class="node"><title>t27</title> 365<polygon style="fill:#90ee90;stroke:green;" points="247,-608 135,-608 131,-604 131,-572 243,-572 247,-576 247,-608"/> 366<polyline style="fill:none;stroke:green;" points="243,-604 131,-604 "/> 367<polyline style="fill:none;stroke:green;" points="243,-604 243,-572 "/> 368<polyline style="fill:none;stroke:green;" points="243,-604 247,-608 "/> 369<text text-anchor="middle" x="189" y="-583.5" style="font-family:Times New Roman;font-size:20.00;">bowtie_run2</text> 370</g> 371<!-- t26->t27 --> 372<g id="edge31" class="edge"><title>t26->t27</title> 373<path style="fill:none;stroke:gray;" d="M192,-634C192,-629 192,-624 191,-618"/> 374<polygon style="fill:gray;stroke:gray;" points="194.478,-617.602 190,-608 187.512,-618.299 194.478,-617.602"/> 375</g> 376<!-- t28 --> 377<g id="node36" class="node"><title>t28</title> 378<polygon style="fill:#90ee90;stroke:green;" points="244,-550 134,-550 130,-546 130,-514 240,-514 244,-518 244,-550"/> 379<polyline style="fill:none;stroke:green;" points="240,-546 130,-546 "/> 380<polyline style="fill:none;stroke:green;" points="240,-546 240,-514 "/> 381<polyline style="fill:none;stroke:green;" points="240,-546 244,-550 "/> 382<text text-anchor="middle" x="187" y="-525.5" style="font-family:Times New Roman;font-size:20.00;">SAM2BAM</text> 383</g> 384<!-- t27->t28 --> 385<g id="edge33" class="edge"><title>t27->t28</title> 386<path style="fill:none;stroke:gray;" d="M188,-572C188,-568 188,-564 188,-560"/> 387<polygon style="fill:gray;stroke:gray;" points="191.5,-560 188,-550 184.5,-560 191.5,-560"/> 388</g> 389<!-- t29 --> 390<g id="node38" class="node"><title>t29</title> 391<polygon style="fill:#90ee90;stroke:green;" points="259.953,-472.774 185,-487.92 110.047,-472.774 110.117,-448.266 259.883,-448.266 259.953,-472.774"/> 392<polygon style="fill:none;stroke:green;" points="263.963,-476.044 185,-492.001 106.037,-476.044 106.128,-444.266 263.872,-444.266 263.963,-476.044"/> 393<text text-anchor="middle" x="185" y="-459.5" style="font-family:Times New Roman;font-size:20.00;">splitby_chr</text> 394</g> 395<!-- t28->t29 --> 396<g id="edge35" class="edge"><title>t28->t29</title> 397<path style="fill:none;stroke:gray;" d="M186,-514C186,-510 186,-506 186,-502"/> 398<polygon style="fill:gray;stroke:gray;" points="189.5,-502 186,-492 182.5,-502 189.5,-502"/> 399</g> 400<!-- t30 --> 401<g id="node40" class="node"><title>t30</title> 402<polygon style="fill:#90ee90;stroke:green;" points="292,-392 80,-392 76,-388 76,-356 288,-356 292,-360 292,-392"/> 403<polyline style="fill:none;stroke:green;" points="288,-388 76,-388 "/> 404<polyline style="fill:none;stroke:green;" points="288,-388 288,-356 "/> 405<polyline style="fill:none;stroke:green;" points="288,-388 292,-392 "/> 406<text text-anchor="middle" x="184" y="-367.5" style="font-family:Times New Roman;font-size:20.00;">create_by_chr_raw_files</text> 407</g> 408<!-- t29->t30 --> 409<g id="edge37" class="edge"><title>t29->t30</title> 410<path style="fill:none;stroke:gray;" d="M185,-444C184,-431 184,-416 184,-402"/> 411<polygon style="fill:gray;stroke:gray;" points="187.5,-402 184,-392 180.5,-402 187.5,-402"/> 412</g> 413<!-- t31 --> 414<g id="node42" class="node"><title>t31</title> 415<polygon style="fill:#90ee90;stroke:green;" points="270,-300 102,-300 98,-296 98,-264 266,-264 270,-268 270,-300"/> 416<polyline style="fill:none;stroke:green;" points="266,-296 98,-296 "/> 417<polyline style="fill:none;stroke:green;" points="266,-296 266,-264 "/> 418<polyline style="fill:none;stroke:green;" points="266,-296 270,-300 "/> 419<text text-anchor="middle" x="184" y="-275.5" style="font-family:Times New Roman;font-size:20.00;">run_by_chr_bowtie</text> 420</g> 421<!-- t30->t31 --> 422<g id="edge39" class="edge"><title>t30->t31</title> 423<path style="fill:none;stroke:gray;" d="M184,-356C184,-343 184,-325 184,-310"/> 424<polygon style="fill:gray;stroke:gray;" points="187.5,-310 184,-300 180.5,-310 187.5,-310"/> 425</g> 426<!-- t32 --> 427<g id="node44" class="node"><title>t32</title> 428<polygon style="fill:#90ee90;stroke:green;" points="287,-234 85,-234 81,-230 81,-198 283,-198 287,-202 287,-234"/> 429<polyline style="fill:none;stroke:green;" points="283,-230 81,-230 "/> 430<polyline style="fill:none;stroke:green;" points="283,-230 283,-198 "/> 431<polyline style="fill:none;stroke:green;" points="283,-230 287,-234 "/> 432<text text-anchor="middle" x="184" y="-209.5" style="font-family:Times New Roman;font-size:20.00;">by_chr_SAM_to_BAM</text> 433</g> 434<!-- t31->t32 --> 435<g id="edge41" class="edge"><title>t31->t32</title> 436<path style="fill:none;stroke:gray;" d="M184,-264C184,-258 184,-251 184,-244"/> 437<polygon style="fill:gray;stroke:gray;" points="187.5,-244 184,-234 180.5,-244 187.5,-244"/> 438</g> 439<!-- t33 --> 440<g id="node48" class="node"><title>t33</title> 441<polygon style="fill:#90ee90;stroke:green;" points="234,-176 138,-176 134,-172 134,-140 230,-140 234,-144 234,-176"/> 442<polyline style="fill:none;stroke:green;" points="230,-172 134,-172 "/> 443<polyline style="fill:none;stroke:green;" points="230,-172 230,-140 "/> 444<polyline style="fill:none;stroke:green;" points="230,-172 234,-176 "/> 445<text text-anchor="middle" x="184" y="-151.5" style="font-family:Times New Roman;font-size:20.00;">ccheckhits</text> 446</g> 447<!-- t32->t33 --> 448<g id="edge45" class="edge"><title>t32->t33</title> 449<path style="fill:none;stroke:gray;" d="M184,-198C184,-194 184,-190 184,-186"/> 450<polygon style="fill:gray;stroke:gray;" points="187.5,-186 184,-176 180.5,-186 187.5,-186"/> 451</g> 452<!-- t2->t33 --> 453<g id="edge95" class="edge"><title>t2->t33</title> 454<path style="fill:none;stroke:gray;" d="M416,-779C413,-779 410,-778 407,-778 244,-755 57,-820 57,-656 57,-656 57,-656 57,-282 57,-244 48,-226 72,-198 80,-189 102,-181 124,-173"/> 455<polygon style="fill:gray;stroke:gray;" points="125.427,-176.226 134,-170 123.416,-169.521 125.427,-176.226"/> 456</g> 457<!-- t23 --> 458<g id="node62" class="node"><title>t23</title> 459<polygon style="fill:#90ee90;stroke:green;" points="697,-748 533,-748 529,-744 529,-712 693,-712 697,-716 697,-748"/> 460<polyline style="fill:none;stroke:green;" points="693,-744 529,-744 "/> 461<polyline style="fill:none;stroke:green;" points="693,-744 693,-712 "/> 462<polyline style="fill:none;stroke:green;" points="693,-744 697,-748 "/> 463<text text-anchor="middle" x="613" y="-723.5" style="font-family:Times New Roman;font-size:20.00;">create_island_seed</text> 464</g> 465<!-- t2->t23 --> 466<g id="edge99" class="edge"><title>t2->t23</title> 467<path style="fill:none;stroke:gray;" d="M540,-778C551,-771 564,-762 576,-754"/> 468<polygon style="fill:gray;stroke:gray;" points="578.621,-756.459 585,-748 574.738,-750.635 578.621,-756.459"/> 469</g> 470<!-- t38 --> 471<g id="node76" class="node"><title>t38</title> 472<polygon style="fill:#90ee90;stroke:green;" points="333.879,-361.794 485,-334.5 636.121,-361.794 635.98,-405.956 334.02,-405.956 333.879,-361.794"/> 473<polygon style="fill:none;stroke:green;" points="329.868,-358.453 485,-330.435 640.132,-358.453 639.967,-409.956 330.033,-409.956 329.868,-358.453"/> 474<text text-anchor="middle" x="485" y="-367.5" style="font-family:Times New Roman;font-size:20.00;">make_karyotype_file_for_circos</text> 475</g> 476<!-- t2->t38 --> 477<g id="edge113" class="edge"><title>t2->t38</title> 478<path style="fill:none;stroke:gray;" d="M512,-778C507,-716 494,-513 488,-420"/> 479<polygon style="fill:gray;stroke:gray;" points="491.478,-419.602 487,-410 484.512,-420.299 491.478,-419.602"/> 480</g> 481<!-- t33->t46 --> 482<g id="edge117" class="edge"><title>t33->t46</title> 483<path style="fill:none;stroke:gray;" d="M234,-143C257,-136 285,-128 309,-121"/> 484<polygon style="fill:gray;stroke:gray;" points="310.427,-124.226 319,-118 308.416,-117.521 310.427,-124.226"/> 485</g> 486<!-- t44 --> 487<g id="node52" class="node"><title>t44</title> 488<polygon style="fill:#90ee90;stroke:green;" points="147,-1368 49,-1368 45,-1364 45,-1332 143,-1332 147,-1336 147,-1368"/> 489<polyline style="fill:none;stroke:green;" points="143,-1364 45,-1364 "/> 490<polyline style="fill:none;stroke:green;" points="143,-1364 143,-1332 "/> 491<polyline style="fill:none;stroke:green;" points="143,-1364 147,-1368 "/> 492<text text-anchor="middle" x="96" y="-1343.5" style="font-family:Times New Roman;font-size:20.00;">velvet_run</text> 493</g> 494<!-- t43->t44 --> 495<g id="edge49" class="edge"><title>t43->t44</title> 496<path style="fill:none;stroke:gray;" d="M116,-1390C114,-1386 111,-1382 109,-1377"/> 497<polygon style="fill:gray;stroke:gray;" points="112.26,-1375.72 105,-1368 105.863,-1378.56 112.26,-1375.72"/> 498</g> 499<!-- t45 --> 500<g id="node54" class="node"><title>t45</title> 501<polygon style="fill:#90ee90;stroke:green;" points="112,-1178 20,-1178 16,-1174 16,-1142 108,-1142 112,-1146 112,-1178"/> 502<polyline style="fill:none;stroke:green;" points="108,-1174 16,-1174 "/> 503<polyline style="fill:none;stroke:green;" points="108,-1174 108,-1142 "/> 504<polyline style="fill:none;stroke:green;" points="108,-1174 112,-1178 "/> 505<text text-anchor="middle" x="64" y="-1153.5" style="font-family:Times New Roman;font-size:20.00;">oases_run</text> 506</g> 507<!-- t44->t45 --> 508<g id="edge51" class="edge"><title>t44->t45</title> 509<path style="fill:none;stroke:gray;" d="M93,-1332C88,-1298 75,-1227 69,-1188"/> 510<polygon 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style="fill:gray;stroke:gray;" points="461.299,-105.512 451,-108 460.602,-112.478 461.299,-105.512"/> 526</g> 527<!-- t19->t22 --> 528<g id="edge57" class="edge"><title>t19->t22</title> 529<path style="fill:none;stroke:gray;" d="M795,-836C783,-830 769,-824 756,-818"/> 530<polygon style="fill:gray;stroke:gray;" points="757.56,-814.863 747,-814 754.717,-821.26 757.56,-814.863"/> 531</g> 532<!-- t19->t46 --> 533<g id="edge125" class="edge"><title>t19->t46</title> 534<path style="fill:none;stroke:gray;" d="M859,-836C885,-814 923,-774 923,-730 923,-730 923,-730 923,-216 923,-158 995,-197 760,-140 706,-126 556,-113 461,-106"/> 535<polygon style="fill:gray;stroke:gray;" points="461.299,-102.512 451,-105 460.602,-109.478 461.299,-102.512"/> 536</g> 537<!-- t22->t23 --> 538<g id="edge59" class="edge"><title>t22->t23</title> 539<path style="fill:none;stroke:gray;" d="M681,-778C671,-771 658,-762 647,-754"/> 540<polygon style="fill:gray;stroke:gray;" points="649.1,-751.2 639,-748 644.9,-756.8 649.1,-751.2"/> 541</g> 542<!-- t23->t34 --> 543<g id="edge101" class="edge"><title>t23->t34</title> 544<path style="fill:none;stroke:gray;" d="M613,-712C613,-703 613,-694 613,-684"/> 545<polygon style="fill:gray;stroke:gray;" points="616.5,-684 613,-674 609.5,-684 616.5,-684"/> 546</g> 547<!-- t35 --> 548<g id="node66" class="node"><title>t35</title> 549<polygon style="fill:#90ee90;stroke:green;" points="864,-608 602,-608 598,-604 598,-572 860,-572 864,-576 864,-608"/> 550<polyline style="fill:none;stroke:green;" points="860,-604 598,-604 "/> 551<polyline style="fill:none;stroke:green;" points="860,-604 860,-572 "/> 552<polyline style="fill:none;stroke:green;" points="860,-604 864,-608 "/> 553<text text-anchor="middle" x="731" y="-583.5" style="font-family:Times New Roman;font-size:20.00;">make_fasta_for_RepeatMasker</text> 554</g> 555<!-- t34->t35 --> 556<g id="edge63" class="edge"><title>t34->t35</title> 557<path style="fill:none;stroke:gray;" d="M645,-638C659,-631 675,-621 689,-613"/> 558<polygon style="fill:gray;stroke:gray;" points="690.958,-615.916 698,-608 687.559,-609.797 690.958,-615.916"/> 559</g> 560<!-- t34->t37 --> 561<g id="edge105" class="edge"><title>t34->t37</title> 562<path style="fill:none;stroke:gray;" d="M602,-638C597,-629 592,-618 589,-608 580,-567 571,-548 593,-514 600,-504 610,-496 620,-489"/> 563<polygon style="fill:gray;stroke:gray;" points="621.958,-491.916 629,-484 618.559,-485.797 621.958,-491.916"/> 564</g> 565<!-- t39 --> 566<g id="node72" class="node"><title>t39</title> 567<polygon style="fill:none;stroke:blue;" points="884,-392 682,-392 678,-388 678,-356 880,-356 884,-360 884,-392"/> 568<polyline style="fill:none;stroke:blue;" points="880,-388 678,-388 "/> 569<polyline style="fill:none;stroke:blue;" points="880,-388 880,-356 "/> 570<polyline style="fill:none;stroke:blue;" points="880,-388 884,-392 "/> 571<text text-anchor="middle" x="781" y="-367.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">remove_simple_repeats</text> 572</g> 573<!-- t34->t39 --> 574<g id="edge109" class="edge"><title>t34->t39</title> 575<path style="fill:none;stroke:gray;" d="M665,-654C733,-650 847,-639 873,-608 926,-544 849,-445 806,-399"/> 576<polygon style="fill:gray;stroke:gray;" points="808.546,-396.596 799,-392 803.596,-401.546 808.546,-396.596"/> 577</g> 578<!-- t40 --> 579<g id="node74" class="node"><title>t40</title> 580<polygon style="fill:none;stroke:blue;" points="750.217,-288.774 659,-303.92 567.783,-288.774 567.868,-264.266 750.132,-264.266 750.217,-288.774"/> 581<polygon style="fill:none;stroke:blue;" points="754.229,-292.162 659,-307.975 563.771,-292.162 563.882,-260.266 754.118,-260.266 754.229,-292.162"/> 582<text text-anchor="middle" x="659" y="-275.5" style="font-family:Times New Roman;font-size:20.00;fill:blue;">report_islands</text> 583</g> 584<!-- t34->t40 --> 585<g id="edge111" class="edge"><title>t34->t40</title> 586<path 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