Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000169370 l18 e 0 nr 1000000 chr ENSMUST00000101640 l18 e 0 nr 1500000 chr ENSMUST00000061450 l18 e 0 nr 2000000 chr ENSMUST00000091560 l18 e 0 nr 2500000 chr ENSMUST00000019290 l18 e 0 nr 3000000 chr ENSMUST00000159610 l18 e 0 nr 3500000 chr ENSMUST00000025930 l18 e 0 nr 4000000 chr ENSMUST00000167270 l18 e 0 nr 4500000 chr ENSMUST00000117150 l18 e 0 nr 5000000 chr ENSMUST00000105840 l18 e 0 nr 5500000 chr ENSMUST00000077290 l18 e 0 nr 6000000 chr ENSMUST00000033000 l18 e 0 nr 6500000 chr ENSMUST00000067880 l18 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 6812365 reads mapping to 3595243 Unique genomic coordinates Making up 106842 groups Consisting of 36524 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000063091 l18 e 1 nr 1000000 chr ENSMUST00000070681 l18 e 1 nr 1500000 chr ENSMUST00000170871 l18 e 1 nr 2000000 chr ENSMUST00000111791 l18 e 1 nr 2500000 chr ENSMUST00000114471 l18 e 1 nr 3000000 chr ENSMUST00000059571 l18 e 1 nr 3500000 chr ENSMUST00000057481 l18 e 1 nr 4000000 chr ENSMUST00000098761 l18 e 1 nr 4500000 chr ENSMUST00000094451 l18 e 1 nr 5000000 chr ENSMUST00000114151 l18 e 1 nr 5500000 chr ENSMUST00000084391 l18 e 1 nr 6000000 chr ENSMUST00000115481 l18 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 6213210 reads mapping to 3542870 Unique genomic coordinates Making up 106077 groups Consisting of 35921 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000170472 l18 e 2 nr 1000000 chr ENSMUST00000041162 l18 e 2 nr 1500000 chr ENSMUST00000143052 l18 e 2 nr 2000000 chr ENSMUST00000076352 l18 e 2 nr 2500000 chr ENSMUST00000048372 l18 e 2 nr 3000000 chr ENSMUST00000088512 l18 e 2 nr 3500000 chr ENSMUST00000115692 l18 e 2 nr 4000000 chr ENSMUST00000112862 l18 e 2 nr 4500000 chr ENSMUST00000029102 l18 e 2 nr 5000000 chr ENSMUST00000094192 l18 e 2 nr 5500000 chr ENSMUST00000060442 l18 e 2 nr 6000000 chr ENSMUST00000019882 l18 e 2 nr 6500000 chr ENSMUST00000166612 l18 e 2 nr 7000000 chr ENSMUST00000063042 l18 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 7182122 reads mapping to 3542067 Unique genomic coordinates Making up 105657 groups Consisting of 36379 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000038213 l18 e 3 nr 1000000 chr ENSMUST00000020383 l18 e 3 nr 1500000 chr ENSMUST00000128483 l18 e 3 nr 2000000 chr ENSMUST00000128483 l18 e 3 nr 2500000 chr ENSMUST00000068853 l18 e 3 nr 3000000 chr ENSMUST00000001253 l18 e 3 nr 3500000 chr ENSMUST00000112283 l18 e 3 nr 4000000 chr ENSMUST00000169803 l18 e 3 nr 4500000 chr ENSMUST00000163123 l18 e 3 nr 5000000 chr ENSMUST00000112553 l18 e 3 nr 5500000 chr ENSMUST00000117123 l18 e 3 nr 6000000 chr ENSMUST00000102973 l18 e 3 nr 6500000 chr ENSMUST00000070203 l18 e 3 nr 7000000 chr ENSMUST00000119443 l18 e 3 nr 7500000 chr ENSMUST00000079323 l18 e 3 nr 8000000 chr ENSMUST00000120493 l18 e 3 nr 8500000 chr ENSMUST00000065353 l18 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 8886030 reads mapping to 3486800 Unique genomic coordinates Making up 103779 groups Consisting of 35596 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000138184 l18 e 4 nr 1000000 chr ENSMUST00000102914 l18 e 4 nr 1500000 chr ENSMUST00000124714 l18 e 4 nr 2000000 chr ENSMUST00000022114 l18 e 4 nr 2500000 chr ENSMUST00000109324 l18 e 4 nr 3000000 chr ENSMUST00000046254 l18 e 4 nr 3500000 chr ENSMUST00000043584 l18 e 4 nr 4000000 chr ENSMUST00000046274 l18 e 4 nr 4500000 chr ENSMUST00000048274 l18 e 4 nr 5000000 chr ENSMUST00000076124 l18 e 4 nr 5500000 chr ENSMUST00000094644 l18 e 4 nr 6000000 chr ENSMUST00000109614 l18 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 6472973 reads mapping to 3608472 Unique genomic coordinates Making up 107944 groups Consisting of 36939 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000171825 l18 e 5 nr 1000000 chr ENSMUST00000144725 l18 e 5 nr 1500000 chr ENSMUST00000037915 l18 e 5 nr 2000000 chr ENSMUST00000035515 l18 e 5 nr 2500000 chr ENSMUST00000110835 l18 e 5 nr 3000000 chr ENSMUST00000023335 l18 e 5 nr 3500000 chr ENSMUST00000115705 l18 e 5 nr 4000000 chr ENSMUST00000147755 l18 e 5 nr 4500000 chr ENSMUST00000154585 l18 e 5 nr 5000000 chr ENSMUST00000030315 l18 e 5 nr 5500000 chr ENSMUST00000036225 l18 e 5 nr 6000000 chr ENSMUST00000166315 l18 e 5 nr 6500000 chr ENSMUST00000057755 l18 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 6932563 reads mapping to 3586433 Unique genomic coordinates Making up 106899 groups Consisting of 36293 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000127206 l18 e 6 nr 1000000 chr ENSMUST00000105436 l18 e 6 nr 1500000 chr ENSMUST00000102756 l18 e 6 nr 2000000 chr ENSMUST00000102756 l18 e 6 nr 2500000 chr ENSMUST00000102756 l18 e 6 nr 3000000 chr ENSMUST00000077156 l18 e 6 nr 3500000 chr ENSMUST00000099166 l18 e 6 nr 4000000 chr ENSMUST00000023806 l18 e 6 nr 4500000 chr ENSMUST00000087026 l18 e 6 nr 5000000 chr ENSMUST00000114906 l18 e 6 nr 5500000 chr ENSMUST00000144856 l18 e 6 nr 6000000 chr ENSMUST00000030076 l18 e 6 nr 6500000 chr ENSMUST00000072476 l18 e 6 nr 7000000 chr ENSMUST00000076226 l18 e 6 nr 7500000 chr ENSMUST00000118136 l18 e 6 nr 8000000 chr ENSMUST00000019616 l18 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 8392028 reads mapping to 3622594 Unique genomic coordinates Making up 108689 groups Consisting of 37233 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000076817 l18 e 7 nr 1000000 chr ENSMUST00000109237 l18 e 7 nr 1500000 chr ENSMUST00000096557 l18 e 7 nr 2000000 chr ENSMUST00000150727 l18 e 7 nr 2500000 chr ENSMUST00000100167 l18 e 7 nr 3000000 chr ENSMUST00000024747 l18 e 7 nr 3500000 chr ENSMUST00000038627 l18 e 7 nr 4000000 chr ENSMUST00000049997 l18 e 7 nr 4500000 chr ENSMUST00000007757 l18 e 7 nr 5000000 chr ENSMUST00000111997 l18 e 7 nr 5500000 chr ENSMUST00000059857 l18 e 7 nr 6000000 chr ENSMUST00000169107 l18 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 6389828 reads mapping to 3592969 Unique genomic coordinates Making up 107531 groups Consisting of 36620 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000092658 l18 e 8 nr 1000000 chr ENSMUST00000108958 l18 e 8 nr 1500000 chr ENSMUST00000150458 l18 e 8 nr 2000000 chr ENSMUST00000161568 l18 e 8 nr 2500000 chr ENSMUST00000073418 l18 e 8 nr 3000000 chr ENSMUST00000066388 l18 e 8 nr 3500000 chr ENSMUST00000170438 l18 e 8 nr 4000000 chr ENSMUST00000081528 l18 e 8 nr 4500000 chr ENSMUST00000106478 l18 e 8 nr 5000000 chr ENSMUST00000153238 l18 e 8 nr 5500000 chr ENSMUST00000161078 l18 e 8 nr 6000000 chr ENSMUST00000068068 l18 e 8 nr 6500000 chr ENSMUST00000108938 l18 e 8 nr 7000000 chr ENSMUST00000062738 l18 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 7146566 reads mapping to 3488066 Unique genomic coordinates Making up 104411 groups Consisting of 35357 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000136479 l18 e 9 nr 1000000 chr ENSMUST00000075329 l18 e 9 nr 1500000 chr ENSMUST00000075329 l18 e 9 nr 2000000 chr ENSMUST00000167069 l18 e 9 nr 2500000 chr ENSMUST00000020649 l18 e 9 nr 3000000 chr ENSMUST00000020649 l18 e 9 nr 3500000 chr ENSMUST00000142499 l18 e 9 nr 4000000 chr ENSMUST00000026119 l18 e 9 nr 4500000 chr ENSMUST00000166369 l18 e 9 nr 5000000 chr ENSMUST00000071869 l18 e 9 nr 5500000 chr ENSMUST00000114589 l18 e 9 nr 6000000 chr ENSMUST00000155329 l18 e 9 nr 6500000 chr ENSMUST00000028279 l18 e 9 nr 7000000 chr ENSMUST00000026859 l18 e 9 nr 7500000 chr ENSMUST00000045029 l18 e 9 nr 8000000 chr ENSMUST00000043529 l18 e 9 nr 8500000 chr ENSMUST00000161619 l18 e 9 nr 9000000 chr ENSMUST00000093529 l18 e 9 nr 9500000 chr ENSMUST00000034279 l18 e 9 nr 10000000 chr ENSMUST00000038579 l18 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 10237647 reads mapping to 3590064 Unique genomic coordinates Making up 107335 groups Consisting of 36522 clusters