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 419420 reads mapping to 240247 Unique genomic coordinates Making up 5955 groups Consisting of 1671 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 439689 reads mapping to 249484 Unique genomic coordinates Making up 6162 groups Consisting of 1702 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 484962 reads mapping to 272306 Unique genomic coordinates Making up 6730 groups Consisting of 1915 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 427781 reads mapping to 253613 Unique genomic coordinates Making up 6397 groups Consisting of 1766 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 444635 reads mapping to 268080 Unique genomic coordinates Making up 6712 groups Consisting of 1816 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 448045 reads mapping to 264427 Unique genomic coordinates Making up 6687 groups Consisting of 1839 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 439096 reads mapping to 254383 Unique genomic coordinates Making up 6280 groups Consisting of 1756 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 482174 reads mapping to 264459 Unique genomic coordinates Making up 6587 groups Consisting of 1827 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 409366 reads mapping to 249715 Unique genomic coordinates Making up 6254 groups Consisting of 1662 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 483592 reads mapping to 251511 Unique genomic coordinates Making up 6271 groups Consisting of 1774 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 446624 reads mapping to 248904 Unique genomic coordinates Making up 6224 groups Consisting of 1708 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000094379-chr7---56135148-56136411 l43 e 11 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 559806 reads mapping to 249725 Unique genomic coordinates Making up 6165 groups Consisting of 1718 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 453421 reads mapping to 259220 Unique genomic coordinates Making up 6383 groups Consisting of 1770 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 419805 reads mapping to 264658 Unique genomic coordinates Making up 6730 groups Consisting of 1842 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 451418 reads mapping to 262770 Unique genomic coordinates Making up 6610 groups Consisting of 1794 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 458731 reads mapping to 263521 Unique genomic coordinates Making up 6436 groups Consisting of 1773 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 446446 reads mapping to 255352 Unique genomic coordinates Making up 6377 groups Consisting of 1788 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 419181 reads mapping to 263578 Unique genomic coordinates Making up 6491 groups Consisting of 1772 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000084715-chr9---123747493-123748618 l45 e 18 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 510336 reads mapping to 256164 Unique genomic coordinates Making up 6374 groups Consisting of 1704 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 670871 reads mapping to 271776 Unique genomic coordinates Making up 6781 groups Consisting of 1908 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 479615 reads mapping to 245906 Unique genomic coordinates Making up 6114 groups Consisting of 1735 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 490528 reads mapping to 241297 Unique genomic coordinates Making up 5953 groups Consisting of 1647 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 428076 reads mapping to 260398 Unique genomic coordinates Making up 6548 groups Consisting of 1787 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000122015-chrX---103555795-103557423 l45 e 23 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 505483 reads mapping to 262621 Unique genomic coordinates Making up 6539 groups Consisting of 1813 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 413260 reads mapping to 268172 Unique genomic coordinates Making up 6734 groups Consisting of 1836 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 390689 reads mapping to 254546 Unique genomic coordinates Making up 6401 groups Consisting of 1795 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 492485 reads mapping to 273276 Unique genomic coordinates Making up 6774 groups Consisting of 1806 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 400221 reads mapping to 249336 Unique genomic coordinates Making up 6289 groups Consisting of 1752 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 421314 reads mapping to 254437 Unique genomic coordinates Making up 6321 groups Consisting of 1712 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 468227 reads mapping to 249089 Unique genomic coordinates Making up 6247 groups Consisting of 1650 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 410157 reads mapping to 270058 Unique genomic coordinates Making up 6715 groups Consisting of 1846 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 470314 reads mapping to 265305 Unique genomic coordinates Making up 6681 groups Consisting of 1952 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 482881 reads mapping to 254103 Unique genomic coordinates Making up 6296 groups Consisting of 1808 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 449520 reads mapping to 256596 Unique genomic coordinates Making up 6483 groups Consisting of 1779 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 433887 reads mapping to 252021 Unique genomic coordinates Making up 6286 groups Consisting of 1786 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170890-chrX---57366056-57367135 l43 e 35 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 511250 reads mapping to 258655 Unique genomic coordinates Making up 6468 groups Consisting of 1739 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 417665 reads mapping to 259296 Unique genomic coordinates Making up 6539 groups Consisting of 1846 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 393543 reads mapping to 245997 Unique genomic coordinates Making up 6225 groups Consisting of 1715 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 444061 reads mapping to 247286 Unique genomic coordinates Making up 6128 groups Consisting of 1666 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000156312-chr8---37635199-37636439 l43 e 39 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 545101 reads mapping to 264625 Unique genomic coordinates Making up 6522 groups Consisting of 1847 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 407309 reads mapping to 256999 Unique genomic coordinates Making up 6537 groups Consisting of 1847 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 269575 Unique genomic coordinates Making up 6783 groups Consisting of 1854 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 445898 reads mapping to 248293 Unique genomic coordinates Making up 6216 groups Consisting of 1676 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 424194 reads mapping to 259245 Unique genomic coordinates Making up 6405 groups Consisting of 1861 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000089062-chrX---35252274-35255044 l43 e 44 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 522833 reads mapping to 260034 Unique genomic coordinates Making up 6429 groups Consisting of 1800 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 450443 reads mapping to 264034 Unique genomic coordinates Making up 6656 groups Consisting of 1789 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 435558 reads mapping to 267586 Unique genomic coordinates Making up 6610 groups Consisting of 1853 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 410800 reads mapping to 249195 Unique genomic coordinates Making up 6296 groups Consisting of 1759 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 433787 reads mapping to 254683 Unique genomic coordinates Making up 6321 groups Consisting of 1772 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 422544 reads mapping to 261481 Unique genomic coordinates Making up 6403 groups Consisting of 1821 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000034543-chr9-+-35082149-35083550 l43 e 50 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 532337 reads mapping to 260171 Unique genomic coordinates Making up 6402 groups Consisting of 1787 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 388235 reads mapping to 244119 Unique genomic coordinates Making up 6130 groups Consisting of 1710 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 469206 reads mapping to 265869 Unique genomic coordinates Making up 6597 groups Consisting of 1828 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 462541 reads mapping to 264343 Unique genomic coordinates Making up 6549 groups Consisting of 1865 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000044532-chr9---106833752-106835954 l45 e 54 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 515578 reads mapping to 266374 Unique genomic coordinates Making up 6675 groups Consisting of 1834 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 438941 reads mapping to 251023 Unique genomic coordinates Making up 6298 groups Consisting of 1677 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 401934 reads mapping to 258729 Unique genomic coordinates Making up 6457 groups Consisting of 1822 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 473185 reads mapping to 265684 Unique genomic coordinates Making up 6730 groups Consisting of 1880 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 403477 reads mapping to 244798 Unique genomic coordinates Making up 6033 groups Consisting of 1782 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 458471 reads mapping to 251999 Unique genomic coordinates Making up 6288 groups Consisting of 1764 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113595-chr9---70305131-70307460 l43 e 60 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 522722 reads mapping to 252654 Unique genomic coordinates Making up 6306 groups Consisting of 1766 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 406556 reads mapping to 250760 Unique genomic coordinates Making up 6194 groups Consisting of 1707 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 463097 reads mapping to 264116 Unique genomic coordinates Making up 6567 groups Consisting of 1853 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 490245 reads mapping to 253967 Unique genomic coordinates Making up 6335 groups Consisting of 1680 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 387121 reads mapping to 260650 Unique genomic coordinates Making up 6524 groups Consisting of 1820 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 433487 reads mapping to 251111 Unique genomic coordinates Making up 6228 groups Consisting of 1704 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 341490 reads mapping to 227784 Unique genomic coordinates Making up 5746 groups Consisting of 1567 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 438544 reads mapping to 256800 Unique genomic coordinates Making up 6481 groups Consisting of 1815 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 463376 reads mapping to 265788 Unique genomic coordinates Making up 6548 groups Consisting of 1836 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 408899 reads mapping to 250153 Unique genomic coordinates Making up 6142 groups Consisting of 1645 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 415520 reads mapping to 247041 Unique genomic coordinates Making up 6081 groups Consisting of 1698 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 401380 reads mapping to 248797 Unique genomic coordinates Making up 6156 groups Consisting of 1654 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 446637 reads mapping to 261440 Unique genomic coordinates Making up 6549 groups Consisting of 1886 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000016680-chr8-+-13122307-13125373 l43 e 73 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 549166 reads mapping to 254657 Unique genomic coordinates Making up 6413 groups Consisting of 1760 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 411461 reads mapping to 261771 Unique genomic coordinates Making up 6528 groups Consisting of 1758 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000108509-chr7-+-16662821-16665675 l43 e 75 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 559802 reads mapping to 256686 Unique genomic coordinates Making up 6450 groups Consisting of 1772 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 424930 reads mapping to 244265 Unique genomic coordinates Making up 6025 groups Consisting of 1673 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 405247 reads mapping to 251229 Unique genomic coordinates Making up 6318 groups Consisting of 1766 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000131906-chrX-+-97806587-97810578 l43 e 78 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 507897 reads mapping to 280302 Unique genomic coordinates Making up 7034 groups Consisting of 1966 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 447814 reads mapping to 254195 Unique genomic coordinates Making up 6238 groups Consisting of 1735 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 418088 reads mapping to 260434 Unique genomic coordinates Making up 6506 groups Consisting of 1754 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000037370-chr5---36363378-36364481 l43 e 81 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 594198 reads mapping to 246248 Unique genomic coordinates Making up 6121 groups Consisting of 1665 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 476636 reads mapping to 259705 Unique genomic coordinates Making up 6436 groups Consisting of 1767 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 434703 reads mapping to 266883 Unique genomic coordinates Making up 6575 groups Consisting of 1786 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 358212 reads mapping to 241193 Unique genomic coordinates Making up 6040 groups Consisting of 1605 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 428861 reads mapping to 261037 Unique genomic coordinates Making up 6628 groups Consisting of 1804 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 414725 reads mapping to 258721 Unique genomic coordinates Making up 6527 groups Consisting of 1796 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 427071 reads mapping to 264640 Unique genomic coordinates Making up 6704 groups Consisting of 1889 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 404750 reads mapping to 253717 Unique genomic coordinates Making up 6351 groups Consisting of 1756 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 381432 reads mapping to 243639 Unique genomic coordinates Making up 6056 groups Consisting of 1680 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000133787-chr9-+-23902440-23903290 l43 e 90 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 558135 reads mapping to 252847 Unique genomic coordinates Making up 6219 groups Consisting of 1742 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 760271 reads mapping to 268125 Unique genomic coordinates Making up 6655 groups Consisting of 1865 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 449793 reads mapping to 253192 Unique genomic coordinates Making up 6307 groups Consisting of 1690 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000113573-chrX---103020940-103022093 l45 e 93 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 505152 reads mapping to 264205 Unique genomic coordinates Making up 6660 groups Consisting of 1894 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 482795 reads mapping to 268449 Unique genomic coordinates Making up 6681 groups Consisting of 1854 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 411877 reads mapping to 246155 Unique genomic coordinates Making up 6229 groups Consisting of 1681 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 474217 reads mapping to 266685 Unique genomic coordinates Making up 6638 groups Consisting of 1819 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 463138 reads mapping to 254007 Unique genomic coordinates Making up 6263 groups Consisting of 1768 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 383063 reads mapping to 255461 Unique genomic coordinates Making up 6401 groups Consisting of 1770 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 440843 reads mapping to 253636 Unique genomic coordinates Making up 6357 groups Consisting of 1754 clusters