Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 463850 reads mapping to 258167 Unique genomic coordinates Making up 6309 groups Consisting of 591 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 465619 reads mapping to 264330 Unique genomic coordinates Making up 6431 groups Consisting of 564 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000034560-chr9-+-50674049-50676402 l43 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 526267 reads mapping to 295685 Unique genomic coordinates Making up 7271 groups Consisting of 695 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 446773 reads mapping to 271705 Unique genomic coordinates Making up 6672 groups Consisting of 584 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026270-chr9-+-123490866-123492004 l45 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 528937 reads mapping to 282092 Unique genomic coordinates Making up 6932 groups Consisting of 625 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000049985-chr6---3425409-3426705 l41 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 632930 reads mapping to 284624 Unique genomic coordinates Making up 7018 groups Consisting of 585 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000122423-chr7-+-50609846-50612306 l43 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 687558 reads mapping to 270489 Unique genomic coordinates Making up 6651 groups Consisting of 564 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000123128-chr9-+-75021259-75022507 l43 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 525900 reads mapping to 281286 Unique genomic coordinates Making up 6925 groups Consisting of 634 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000077706-chr9---121495421-121496608 l45 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 516159 reads mapping to 267154 Unique genomic coordinates Making up 6573 groups Consisting of 592 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000159483-chr5-+-138729924-138733209 l45 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 579137 reads mapping to 266494 Unique genomic coordinates Making up 6555 groups Consisting of 579 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000107453-chr7---81472246-81473410 l43 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 719494 reads mapping to 264480 Unique genomic coordinates Making up 6599 groups Consisting of 516 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000118899-chrX-+-107105560-107107111 l45 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 506139 reads mapping to 271295 Unique genomic coordinates Making up 6640 groups Consisting of 607 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000150490-chr11-+-96122426-96126012 l44 e 12 nr 1000000 chr ENSMUST00000102534-chr2---117105729-117108912 l45 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1188119 reads mapping to 282463 Unique genomic coordinates Making up 6929 groups Consisting of 609 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161796-chr9---83003555-83005213 l43 e 13 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 519652 reads mapping to 280529 Unique genomic coordinates Making up 6972 groups Consisting of 602 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000056237-chr8-+-80082278-80083514 l43 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 562375 reads mapping to 286966 Unique genomic coordinates Making up 7000 groups Consisting of 596 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142916-chr7---51052290-51053315 l43 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 572014 reads mapping to 285090 Unique genomic coordinates Making up 7089 groups Consisting of 660 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000060208-chr2-+-70075374-70077516 l43 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 842374 reads mapping to 272771 Unique genomic coordinates Making up 6895 groups Consisting of 588 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 486040 reads mapping to 280069 Unique genomic coordinates Making up 6812 groups Consisting of 613 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000149811-chrX-+-140797908-140800018 l45 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 503075 reads mapping to 274585 Unique genomic coordinates Making up 6831 groups Consisting of 618 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133010-chr9---24423048-24424119 l43 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 531128 reads mapping to 290601 Unique genomic coordinates Making up 7117 groups Consisting of 634 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 495968 reads mapping to 262693 Unique genomic coordinates Making up 6497 groups Consisting of 537 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 492645 reads mapping to 257758 Unique genomic coordinates Making up 6256 groups Consisting of 547 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000080751-chr15---84209635-84215322 l44 e 22 nr 1000000 chr ENSMUST00000066193-chr18-+-52853333-52855322 l44 e 22 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1306148 reads mapping to 278614 Unique genomic coordinates Making up 6896 groups Consisting of 582 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 485110 reads mapping to 279162 Unique genomic coordinates Making up 6943 groups Consisting of 563 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025774-chr19---5283143-5285224 l42 e 24 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 887415 reads mapping to 289444 Unique genomic coordinates Making up 7122 groups Consisting of 646 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000150161-chrX-+-98846979-98849925 l43 e 25 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 504478 reads mapping to 272904 Unique genomic coordinates Making up 6706 groups Consisting of 582 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000128656-chr2-+-138250925-138252026 l45 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 678766 reads mapping to 296714 Unique genomic coordinates Making up 7286 groups Consisting of 660 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 485877 reads mapping to 270600 Unique genomic coordinates Making up 6669 groups Consisting of 601 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 498393 reads mapping to 274941 Unique genomic coordinates Making up 6781 groups Consisting of 589 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135086-chrX-+-163120617-163121829 l45 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 500980 reads mapping to 271404 Unique genomic coordinates Making up 6732 groups Consisting of 603 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000040416-chr8---113498896-113501530 l45 e 30 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 547508 reads mapping to 288991 Unique genomic coordinates Making up 7188 groups Consisting of 610 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000141634-chrX-+-7201797-7210831 l41 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 587862 reads mapping to 286361 Unique genomic coordinates Making up 7029 groups Consisting of 661 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 433925 reads mapping to 269690 Unique genomic coordinates Making up 6687 groups Consisting of 582 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000124321-chrX-+-72679317-72682033 l43 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 506430 reads mapping to 279952 Unique genomic coordinates Making up 6884 groups Consisting of 584 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000028056-chr2---13208108-13209834 l43 e 34 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 682182 reads mapping to 268561 Unique genomic coordinates Making up 6614 groups Consisting of 561 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000034775-chr9---62639639-62646035 l43 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 526470 reads mapping to 278059 Unique genomic coordinates Making up 6748 groups Consisting of 625 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000144831-chrX-+-121521251-121524136 l45 e 36 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 503377 reads mapping to 280804 Unique genomic coordinates Making up 6951 groups Consisting of 606 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 460208 reads mapping to 267476 Unique genomic coordinates Making up 6623 groups Consisting of 555 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000138912-chr5-+-34886014-34887438 l43 e 38 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 618013 reads mapping to 273353 Unique genomic coordinates Making up 6669 groups Consisting of 571 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000156520-chr9-+-122273754-122274839 l45 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 512300 reads mapping to 281153 Unique genomic coordinates Making up 6954 groups Consisting of 625 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 477625 reads mapping to 273832 Unique genomic coordinates Making up 6758 groups Consisting of 614 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 472700 reads mapping to 290109 Unique genomic coordinates Making up 7223 groups Consisting of 632 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 447966 reads mapping to 263819 Unique genomic coordinates Making up 6457 groups Consisting of 556 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113873-chrX---92266012-92267143 l43 e 43 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 506342 reads mapping to 282188 Unique genomic coordinates Making up 6983 groups Consisting of 604 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000123128-chr9-+-75041246-75042444 l43 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 534309 reads mapping to 279781 Unique genomic coordinates Making up 6845 groups Consisting of 617 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 471007 reads mapping to 279519 Unique genomic coordinates Making up 6949 groups Consisting of 610 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035115-chr9-+-121568785-121571146 l45 e 46 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 514017 reads mapping to 284364 Unique genomic coordinates Making up 7068 groups Consisting of 591 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 477550 reads mapping to 265154 Unique genomic coordinates Making up 6588 groups Consisting of 561 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000003386-chr9-+-20807181-20808348 l43 e 48 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 532080 reads mapping to 268856 Unique genomic coordinates Making up 6611 groups Consisting of 552 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000044532-chr9---106898725-106899849 l45 e 49 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 515182 reads mapping to 282772 Unique genomic coordinates Making up 6922 groups Consisting of 655 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000001720-chr8-+-112514337-112517050 l45 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 536096 reads mapping to 275899 Unique genomic coordinates Making up 6770 groups Consisting of 569 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000130794-chrX---154234909-154235951 l45 e 51 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 503297 reads mapping to 265452 Unique genomic coordinates Making up 6538 groups Consisting of 583 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000173193-chr6---58902944-58907352 l43 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 584488 reads mapping to 287485 Unique genomic coordinates Making up 7074 groups Consisting of 623 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000173168-chr8-+-126564566-126565653 l45 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 544539 reads mapping to 280686 Unique genomic coordinates Making up 6917 groups Consisting of 619 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000126941-chr7-+-72791864-72793054 l43 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 577054 reads mapping to 284753 Unique genomic coordinates Making up 7040 groups Consisting of 611 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 449392 reads mapping to 267574 Unique genomic coordinates Making up 6619 groups Consisting of 560 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 468131 reads mapping to 279478 Unique genomic coordinates Making up 6867 groups Consisting of 627 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035043-chr9---99383019-99384957 l43 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 517021 reads mapping to 281938 Unique genomic coordinates Making up 7065 groups Consisting of 597 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 495554 reads mapping to 262632 Unique genomic coordinates Making up 6476 groups Consisting of 598 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000146801-chrX-+-133290533-133291659 l45 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 506785 reads mapping to 266020 Unique genomic coordinates Making up 6570 groups Consisting of 576 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000001792-chr7---90821044-90822260 l43 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 556507 reads mapping to 270835 Unique genomic coordinates Making up 6713 groups Consisting of 583 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 461382 reads mapping to 270797 Unique genomic coordinates Making up 6685 groups Consisting of 614 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000031727-chr5-+-137960108-137969162 l45 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 604499 reads mapping to 283137 Unique genomic coordinates Making up 6983 groups Consisting of 582 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000136857-chr9---109992305-109996163 l45 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 511938 reads mapping to 270994 Unique genomic coordinates Making up 6712 groups Consisting of 568 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113108-chrX---132982646-132984564 l45 e 64 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 503107 reads mapping to 287070 Unique genomic coordinates Making up 7087 groups Consisting of 697 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166125-chrX-+-137466504-137468165 l45 e 65 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 503564 reads mapping to 266888 Unique genomic coordinates Making up 6486 groups Consisting of 583 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 446683 reads mapping to 243854 Unique genomic coordinates Making up 6026 groups Consisting of 535 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 493922 reads mapping to 271878 Unique genomic coordinates Making up 6684 groups Consisting of 582 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 495741 reads mapping to 279946 Unique genomic coordinates Making up 6990 groups Consisting of 581 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 483926 reads mapping to 265258 Unique genomic coordinates Making up 6470 groups Consisting of 563 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 455654 reads mapping to 265403 Unique genomic coordinates Making up 6600 groups Consisting of 581 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000052135-chr7-+-130139957-130146071 l45 e 71 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 562388 reads mapping to 270134 Unique genomic coordinates Making up 6526 groups Consisting of 573 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 486680 reads mapping to 280118 Unique genomic coordinates Making up 6914 groups Consisting of 593 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169350-chr6-+-48439197-48449273 l43 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 592187 reads mapping to 273658 Unique genomic coordinates Making up 6819 groups Consisting of 582 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000093200-chr8-+-108210174-108220174 l45 e 74 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 543802 reads mapping to 276563 Unique genomic coordinates Making up 6734 groups Consisting of 600 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000094105-chr7---115302432-115303375 l45 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 546235 reads mapping to 280530 Unique genomic coordinates Making up 6975 groups Consisting of 654 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000001319-chr8---8617434-8621476 l41 e 76 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 546775 reads mapping to 264587 Unique genomic coordinates Making up 6550 groups Consisting of 535 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 448030 reads mapping to 273045 Unique genomic coordinates Making up 6784 groups Consisting of 620 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000121949-chr8-+-90663291-90664378 l43 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 537812 reads mapping to 297915 Unique genomic coordinates Making up 7362 groups Consisting of 681 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000075578-chr8---126481899-126483079 l45 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 533573 reads mapping to 272028 Unique genomic coordinates Making up 6799 groups Consisting of 578 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000164960-chr6-+-118016403-118016980 l45 e 80 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 634860 reads mapping to 281142 Unique genomic coordinates Making up 6976 groups Consisting of 583 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035571-chr5-+-146920119-146921281 l45 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 586943 reads mapping to 262568 Unique genomic coordinates Making up 6491 groups Consisting of 559 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000058098-chrX---153985756-153989582 l45 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 502418 reads mapping to 279527 Unique genomic coordinates Making up 6927 groups Consisting of 614 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000131381-chr4---124412974-124414383 l45 e 83 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 721458 reads mapping to 288992 Unique genomic coordinates Making up 6996 groups Consisting of 660 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 445039 reads mapping to 259738 Unique genomic coordinates Making up 6392 groups Consisting of 551 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000034470-chr9---26819810-26820985 l43 e 85 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 529967 reads mapping to 280000 Unique genomic coordinates Making up 6853 groups Consisting of 584 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000044532-chr9---107061246-107062286 l45 e 86 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 550379 reads mapping to 285637 Unique genomic coordinates Making up 7109 groups Consisting of 670 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000121595-chr8-+-71322766-71323387 l43 e 87 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 559357 reads mapping to 286520 Unique genomic coordinates Making up 7107 groups Consisting of 637 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000115561-chrX-+-8451379-8453588 l41 e 88 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 512363 reads mapping to 269576 Unique genomic coordinates Making up 6660 groups Consisting of 578 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 439231 reads mapping to 259502 Unique genomic coordinates Making up 6446 groups Consisting of 581 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000166802-chr8-+-97464905-97467190 l43 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 546776 reads mapping to 274643 Unique genomic coordinates Making up 6698 groups Consisting of 636 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000051049-chr6---121337252-121338391 l45 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 588270 reads mapping to 288753 Unique genomic coordinates Making up 7076 groups Consisting of 636 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 488559 reads mapping to 273323 Unique genomic coordinates Making up 6714 groups Consisting of 598 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000098060-chr7---130449389-130451093 l45 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 566290 reads mapping to 285949 Unique genomic coordinates Making up 7144 groups Consisting of 610 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000033755-chrX-+-160887887-160888994 l45 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 500749 reads mapping to 288578 Unique genomic coordinates Making up 7116 groups Consisting of 641 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035083-chr9---111507314-111508395 l45 e 95 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 519328 reads mapping to 265029 Unique genomic coordinates Making up 6466 groups Consisting of 584 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000026585-chr7-+-148661139-148661896 l45 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 554403 reads mapping to 288646 Unique genomic coordinates Making up 7036 groups Consisting of 617 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000057972-chr9-+-67779747-67780897 l43 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 523752 reads mapping to 270580 Unique genomic coordinates Making up 6685 groups Consisting of 604 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 478319 reads mapping to 274699 Unique genomic coordinates Making up 6673 groups Consisting of 613 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 452108 reads mapping to 267923 Unique genomic coordinates Making up 6598 groups Consisting of 554 clusters