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 472989 reads mapping to 270935 Unique genomic coordinates Making up 6989 groups Consisting of 1991 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 495526 reads mapping to 280924 Unique genomic coordinates Making up 7317 groups Consisting of 2061 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000118009-chr8-+-69406842-69408002 l43 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 545303 reads mapping to 306248 Unique genomic coordinates Making up 7920 groups Consisting of 2248 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 481717 reads mapping to 284759 Unique genomic coordinates Making up 7432 groups Consisting of 2094 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000117062-chrX-+-151672041-151672804 l45 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 502130 reads mapping to 301672 Unique genomic coordinates Making up 7846 groups Consisting of 2190 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000079945-chrX---153596618-153600705 l45 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 503530 reads mapping to 297769 Unique genomic coordinates Making up 7806 groups Consisting of 2191 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 493994 reads mapping to 285787 Unique genomic coordinates Making up 7284 groups Consisting of 2061 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000077816-chr8---96057908-96059607 l43 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 543469 reads mapping to 297426 Unique genomic coordinates Making up 7629 groups Consisting of 2170 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 461898 reads mapping to 280831 Unique genomic coordinates Making up 7330 groups Consisting of 1988 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000121963-chr9---105946056-105947109 l45 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 542767 reads mapping to 282823 Unique genomic coordinates Making up 7283 groups Consisting of 2108 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000112683-chrX---147521637-147526810 l45 e 10 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 502794 reads mapping to 280035 Unique genomic coordinates Making up 7317 groups Consisting of 2059 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000030841-chr5-+-23646469-23647611 l43 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 626267 reads mapping to 281134 Unique genomic coordinates Making up 7196 groups Consisting of 2049 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000119502-chrX---115811404-115812512 l45 e 12 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 510190 reads mapping to 291667 Unique genomic coordinates Making up 7472 groups Consisting of 2061 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 473315 reads mapping to 297769 Unique genomic coordinates Making up 7827 groups Consisting of 2242 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000132664-chrX---131088438-131092014 l45 e 14 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 508819 reads mapping to 295775 Unique genomic coordinates Making up 7670 groups Consisting of 2131 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000123530-chr9---103164860-103166015 l45 e 15 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 515644 reads mapping to 296580 Unique genomic coordinates Making up 7533 groups Consisting of 2154 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000112622-chrX-+-148297916-148299816 l45 e 16 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 502020 reads mapping to 286866 Unique genomic coordinates Making up 7408 groups Consisting of 2134 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 473080 reads mapping to 296430 Unique genomic coordinates Making up 7595 groups Consisting of 2127 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000039431-chr7---85622250-85623318 l43 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 571675 reads mapping to 287727 Unique genomic coordinates Making up 7427 groups Consisting of 2024 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000073488-chr7---51804986-51809319 l43 e 19 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 751832 reads mapping to 305798 Unique genomic coordinates Making up 7956 groups Consisting of 2241 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000057972-chr9-+-67810356-67812620 l43 e 20 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 537227 reads mapping to 276426 Unique genomic coordinates Making up 7092 groups Consisting of 2077 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000122324-chr8-+-22448841-22449621 l43 e 21 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 550918 reads mapping to 271607 Unique genomic coordinates Making up 6992 groups Consisting of 1967 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 482555 reads mapping to 292782 Unique genomic coordinates Making up 7629 groups Consisting of 2148 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000025202-chr7-+-53682216-53688723 l43 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 568955 reads mapping to 295676 Unique genomic coordinates Making up 7624 groups Consisting of 2124 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 467062 reads mapping to 301444 Unique genomic coordinates Making up 7814 groups Consisting of 2206 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 440944 reads mapping to 286255 Unique genomic coordinates Making up 7432 groups Consisting of 2110 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000151977-chr9---29769930-29770726 l43 e 26 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 554226 reads mapping to 307708 Unique genomic coordinates Making up 7951 groups Consisting of 2168 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 450881 reads mapping to 280383 Unique genomic coordinates Making up 7319 groups Consisting of 2089 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 474343 reads mapping to 286193 Unique genomic coordinates Making up 7393 groups Consisting of 2075 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000081232-chr8-+-120022191-120022829 l45 e 29 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 526457 reads mapping to 280776 Unique genomic coordinates Making up 7301 groups Consisting of 1990 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 462537 reads mapping to 303295 Unique genomic coordinates Making up 7831 groups Consisting of 2200 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000035203-chr9-+-107813351-107820731 l45 e 31 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 528788 reads mapping to 298640 Unique genomic coordinates Making up 7767 groups Consisting of 2307 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000141021-chr8---67207891-67208932 l43 e 32 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 542937 reads mapping to 285808 Unique genomic coordinates Making up 7365 groups Consisting of 2117 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165805-chrX-+-130459846-130462233 l45 e 33 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 505392 reads mapping to 288542 Unique genomic coordinates Making up 7578 groups Consisting of 2099 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 488683 reads mapping to 283539 Unique genomic coordinates Making up 7359 groups Consisting of 2136 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000032336-chr6---136588138-136590235 l45 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 573523 reads mapping to 290928 Unique genomic coordinates Making up 7546 groups Consisting of 2060 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 471201 reads mapping to 291515 Unique genomic coordinates Making up 7618 groups Consisting of 2196 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 443522 reads mapping to 276875 Unique genomic coordinates Making up 7224 groups Consisting of 2045 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 499771 reads mapping to 278016 Unique genomic coordinates Making up 7181 groups Consisting of 1976 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000044642-chr5---140191160-140195839 l45 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 611805 reads mapping to 297621 Unique genomic coordinates Making up 7658 groups Consisting of 2194 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 459617 reads mapping to 289149 Unique genomic coordinates Making up 7648 groups Consisting of 2191 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000150434-chrX---105950255-105952241 l45 e 41 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 504235 reads mapping to 303211 Unique genomic coordinates Making up 7908 groups Consisting of 2211 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000101113-chrX-+-157591265-157592342 l45 e 42 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 500644 reads mapping to 279288 Unique genomic coordinates Making up 7287 groups Consisting of 2041 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 477833 reads mapping to 291452 Unique genomic coordinates Making up 7489 groups Consisting of 2204 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165600-chr7-+-98063470-98064544 l43 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 588711 reads mapping to 292450 Unique genomic coordinates Making up 7490 groups Consisting of 2152 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000142132-chrX-+-135492389-135493445 l45 e 45 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 506024 reads mapping to 296614 Unique genomic coordinates Making up 7707 groups Consisting of 2132 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 490414 reads mapping to 301098 Unique genomic coordinates Making up 7725 groups Consisting of 2207 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 462895 reads mapping to 280503 Unique genomic coordinates Making up 7323 groups Consisting of 2070 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 487872 reads mapping to 286444 Unique genomic coordinates Making up 7364 groups Consisting of 2100 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 475682 reads mapping to 293886 Unique genomic coordinates Making up 7465 groups Consisting of 2157 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000130454-chr6---128180110-128181250 l45 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 598287 reads mapping to 292428 Unique genomic coordinates Making up 7573 groups Consisting of 2100 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 438013 reads mapping to 274824 Unique genomic coordinates Making up 7153 groups Consisting of 2023 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000159099-chr9---77947095-77948152 l43 e 52 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 527694 reads mapping to 299095 Unique genomic coordinates Making up 7737 groups Consisting of 2148 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000115512-chrX---11613866-11616953 l43 e 53 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 519548 reads mapping to 296747 Unique genomic coordinates Making up 7636 groups Consisting of 2211 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000167323-chr6-+-134933100-134936854 l45 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 578434 reads mapping to 299559 Unique genomic coordinates Making up 7813 groups Consisting of 2166 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 493198 reads mapping to 282068 Unique genomic coordinates Making up 7349 groups Consisting of 2015 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 453585 reads mapping to 291219 Unique genomic coordinates Making up 7565 groups Consisting of 2158 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000093271-chr8-+-97508503-97509057 l43 e 57 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 531562 reads mapping to 299175 Unique genomic coordinates Making up 7889 groups Consisting of 2263 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 454674 reads mapping to 275536 Unique genomic coordinates Making up 7009 groups Consisting of 2087 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000128982-chr9---118813989-118815859 l45 e 59 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 515168 reads mapping to 283312 Unique genomic coordinates Making up 7323 groups Consisting of 2081 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000094705-chr7---25368857-25372660 l43 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 584369 reads mapping to 284049 Unique genomic coordinates Making up 7331 groups Consisting of 2088 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 458714 reads mapping to 281930 Unique genomic coordinates Making up 7229 groups Consisting of 2028 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000145410-chr9-+-96917912-96922462 l43 e 62 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 521333 reads mapping to 296749 Unique genomic coordinates Making up 7670 groups Consisting of 2216 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000163062-chr8-+-14962018-14963163 l43 e 63 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 549732 reads mapping to 285350 Unique genomic coordinates Making up 7363 groups Consisting of 1994 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 437190 reads mapping to 293338 Unique genomic coordinates Making up 7640 groups Consisting of 2168 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 489219 reads mapping to 282653 Unique genomic coordinates Making up 7279 groups Consisting of 2048 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 385845 reads mapping to 256599 Unique genomic coordinates Making up 6733 groups Consisting of 1870 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 493118 reads mapping to 288688 Unique genomic coordinates Making up 7492 groups Consisting of 2132 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000034984-chr9---96477392-96478468 l43 e 68 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 521016 reads mapping to 298962 Unique genomic coordinates Making up 7688 groups Consisting of 2192 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 460958 reads mapping to 281376 Unique genomic coordinates Making up 7179 groups Consisting of 1951 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 467433 reads mapping to 277785 Unique genomic coordinates Making up 7148 groups Consisting of 2034 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 453371 reads mapping to 280234 Unique genomic coordinates Making up 7272 groups Consisting of 1989 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113104-chrX-+-133063876-133065172 l45 e 72 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 504415 reads mapping to 294076 Unique genomic coordinates Making up 7611 groups Consisting of 2216 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000165534-chr7---140206150-140207373 l45 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 616127 reads mapping to 286953 Unique genomic coordinates Making up 7481 groups Consisting of 2093 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 463828 reads mapping to 294437 Unique genomic coordinates Making up 7619 groups Consisting of 2112 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000098013-chr4---70064008-70065075 l43 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 627722 reads mapping to 288827 Unique genomic coordinates Making up 7511 groups Consisting of 2088 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 478460 reads mapping to 274743 Unique genomic coordinates Making up 7036 groups Consisting of 1990 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 457526 reads mapping to 282591 Unique genomic coordinates Making up 7359 groups Consisting of 2084 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000085077-chr7---91509564-91510678 l43 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 570863 reads mapping to 314897 Unique genomic coordinates Making up 8204 groups Consisting of 2332 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000151941-chrX-+-148009679-148010379 l45 e 79 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 503475 reads mapping to 285642 Unique genomic coordinates Making up 7351 groups Consisting of 2071 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 471302 reads mapping to 292943 Unique genomic coordinates Making up 7624 groups Consisting of 2109 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000102517-chr2-+-119155852-119159081 l45 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 663334 reads mapping to 276993 Unique genomic coordinates Making up 7204 groups Consisting of 2011 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000070326-chr9-+-83746194-83747282 l43 e 82 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 535241 reads mapping to 292284 Unique genomic coordinates Making up 7565 groups Consisting of 2120 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 490118 reads mapping to 300372 Unique genomic coordinates Making up 7656 groups Consisting of 2159 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 404631 reads mapping to 271342 Unique genomic coordinates Making up 7074 groups Consisting of 1935 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 483714 reads mapping to 294255 Unique genomic coordinates Making up 7724 groups Consisting of 2136 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 468113 reads mapping to 291236 Unique genomic coordinates Making up 7612 groups Consisting of 2132 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 481364 reads mapping to 297769 Unique genomic coordinates Making up 7756 groups Consisting of 2234 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 455905 reads mapping to 285047 Unique genomic coordinates Making up 7355 groups Consisting of 2066 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 430849 reads mapping to 274443 Unique genomic coordinates Making up 7092 groups Consisting of 2002 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000131541-chr7-+-103877359-103880790 l45 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 625496 reads mapping to 284283 Unique genomic coordinates Making up 7312 groups Consisting of 2076 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000149002-chr4-+-140873897-140875491 l45 e 91 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 847777 reads mapping to 301704 Unique genomic coordinates Making up 7764 groups Consisting of 2212 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000045898-chrX-+-90979604-90980792 l43 e 92 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 505972 reads mapping to 284710 Unique genomic coordinates Making up 7365 groups Consisting of 2009 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000124057-chr7-+-94394606-94396593 l43 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 567123 reads mapping to 297226 Unique genomic coordinates Making up 7780 groups Consisting of 2237 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000135050-chr9---61801288-61804594 l43 e 94 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 542975 reads mapping to 302423 Unique genomic coordinates Making up 7850 groups Consisting of 2221 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 462848 reads mapping to 276734 Unique genomic coordinates Making up 7287 groups Consisting of 2005 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000131007-chr9-+-57965622-57966796 l43 e 96 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 533260 reads mapping to 300043 Unique genomic coordinates Making up 7815 groups Consisting of 2207 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000034619-chr9---35595635-35597697 l43 e 97 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 521960 reads mapping to 285919 Unique genomic coordinates Making up 7320 groups Consisting of 2087 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 432864 reads mapping to 287816 Unique genomic coordinates Making up 7460 groups Consisting of 2131 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 496088 reads mapping to 285533 Unique genomic coordinates Making up 7362 groups Consisting of 2061 clusters