Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000161260 l18 e 0 nr 1000000 chr ENSMUST00000118330 l18 e 0 nr 1500000 chr ENSMUST00000169150 l18 e 0 nr 2000000 chr ENSMUST00000063220 l18 e 0 nr 2500000 chr ENSMUST00000147320 l18 e 0 nr 3000000 chr ENSMUST00000129520 l18 e 0 nr 3500000 chr ENSMUST00000129390 l18 e 0 nr 4000000 chr ENSMUST00000148920 l18 e 0 nr 4500000 chr ENSMUST00000148000 l18 e 0 nr 5000000 chr ENSMUST00000104190 l18 e 0 nr 5500000 chr ENSMUST00000157710 l18 e 0 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1287764 reads mapping to 654784 Unique genomic coordinates Making up 13933 groups Consisting of 6765 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000123241 l18 e 1 nr 1000000 chr ENSMUST00000141891 l18 e 1 nr 1500000 chr ENSMUST00000146301 l18 e 1 nr 2000000 chr ENSMUST00000148131 l18 e 1 nr 2500000 chr ENSMUST00000137001 l18 e 1 nr 3000000 chr ENSMUST00000132611 l18 e 1 nr 3500000 chr ENSMUST00000120941 l18 e 1 nr 4000000 chr ENSMUST00000123941 l18 e 1 nr 4500000 chr ENSMUST00000123731 l18 e 1 nr 5000000 chr ENSMUST00000149171 l18 e 1 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1328144 reads mapping to 642140 Unique genomic coordinates Making up 13632 groups Consisting of 6790 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000171012 l18 e 2 nr 1000000 chr ENSMUST00000118302 l18 e 2 nr 1500000 chr ENSMUST00000153762 l18 e 2 nr 2000000 chr ENSMUST00000173292 l18 e 2 nr 2500000 chr ENSMUST00000125512 l18 e 2 nr 3000000 chr ENSMUST00000167752 l18 e 2 nr 3500000 chr ENSMUST00000134202 l18 e 2 nr 4000000 chr ENSMUST00000136102 l18 e 2 nr 4500000 chr ENSMUST00000159482 l18 e 2 nr 5000000 chr ENSMUST00000146352 l18 e 2 nr 5500000 chr ENSMUST00000122102 l18 e 2 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1476312 reads mapping to 685353 Unique genomic coordinates Making up 14179 groups Consisting of 7135 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000154303 l18 e 3 nr 1000000 chr ENSMUST00000141143 l18 e 3 nr 1500000 chr ENSMUST00000131193 l18 e 3 nr 2000000 chr ENSMUST00000134163 l18 e 3 nr 2500000 chr ENSMUST00000129913 l18 e 3 nr 3000000 chr ENSMUST00000136473 l18 e 3 nr 3500000 chr ENSMUST00000119793 l18 e 3 nr 4000000 chr ENSMUST00000126003 l18 e 3 nr 4500000 chr ENSMUST00000151813 l18 e 3 nr 5000000 chr ENSMUST00000159113 l18 e 3 nr 5500000 chr ENSMUST00000131143 l18 e 3 nr 6000000 chr ENSMUST00000124213 l18 e 3 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1292272 reads mapping to 650884 Unique genomic coordinates Making up 14052 groups Consisting of 6681 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000138974 l18 e 4 nr 1000000 chr ENSMUST00000171214 l18 e 4 nr 1500000 chr ENSMUST00000161944 l18 e 4 nr 2000000 chr ENSMUST00000129814 l18 e 4 nr 2500000 chr ENSMUST00000140044 l18 e 4 nr 3000000 chr ENSMUST00000142014 l18 e 4 nr 3500000 chr ENSMUST00000079844 l18 e 4 nr 4000000 chr ENSMUST00000132544 l18 e 4 nr 4500000 chr ENSMUST00000141164 l18 e 4 nr 5000000 chr ENSMUST00000125054 l18 e 4 nr 5500000 chr ENSMUST00000153124 l18 e 4 nr 6000000 chr ENSMUST00000084824 l18 e 4 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1672820 reads mapping to 630954 Unique genomic coordinates Making up 13353 groups Consisting of 6701 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000125055 l18 e 5 nr 1000000 chr ENSMUST00000154475 l18 e 5 nr 1500000 chr ENSMUST00000085735 l18 e 5 nr 2000000 chr ENSMUST00000160655 l18 e 5 nr 2500000 chr ENSMUST00000147265 l18 e 5 nr 3000000 chr ENSMUST00000147265 l18 e 5 nr 3500000 chr ENSMUST00000126755 l18 e 5 nr 4000000 chr ENSMUST00000118185 l18 e 5 nr 4500000 chr ENSMUST00000116365 l18 e 5 nr 5000000 chr ENSMUST00000133445 l18 e 5 nr 5500000 chr ENSMUST00000150075 l18 e 5 nr 6000000 chr ENSMUST00000132395 l18 e 5 nr 6500000 chr ENSMUST00000159935 l18 e 5 nr 7000000 chr ENSMUST00000118945 l18 e 5 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1530790 reads mapping to 658049 Unique genomic coordinates Making up 14106 groups Consisting of 6840 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000127386 l18 e 6 nr 1000000 chr ENSMUST00000169576 l18 e 6 nr 1500000 chr ENSMUST00000118506 l18 e 6 nr 2000000 chr ENSMUST00000129956 l18 e 6 nr 2500000 chr ENSMUST00000150926 l18 e 6 nr 3000000 chr ENSMUST00000037776 l18 e 6 nr 3500000 chr ENSMUST00000037776 l18 e 6 nr 4000000 chr ENSMUST00000164426 l18 e 6 nr 4500000 chr ENSMUST00000048086 l18 e 6 nr 5000000 chr ENSMUST00000131666 l18 e 6 nr 5500000 chr ENSMUST00000117116 l18 e 6 nr 6000000 chr ENSMUST00000130096 l18 e 6 nr 6500000 chr ENSMUST00000156276 l18 e 6 nr 7000000 chr ENSMUST00000132456 l18 e 6 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1475431 reads mapping to 648807 Unique genomic coordinates Making up 13806 groups Consisting of 6875 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000156487 l18 e 7 nr 1000000 chr ENSMUST00000169937 l18 e 7 nr 1500000 chr ENSMUST00000133217 l18 e 7 nr 2000000 chr ENSMUST00000162137 l18 e 7 nr 2500000 chr ENSMUST00000153927 l18 e 7 nr 3000000 chr ENSMUST00000054477 l18 e 7 nr 3500000 chr ENSMUST00000134977 l18 e 7 nr 4000000 chr ENSMUST00000145727 l18 e 7 nr 4500000 chr ENSMUST00000131757 l18 e 7 nr 5000000 chr ENSMUST00000159827 l18 e 7 nr 5500000 chr ENSMUST00000136577 l18 e 7 nr 6000000 chr ENSMUST00000144377 l18 e 7 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1403563 reads mapping to 642500 Unique genomic coordinates Making up 13669 groups Consisting of 6685 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000147218 l18 e 8 nr 1000000 chr ENSMUST00000132408 l18 e 8 nr 1500000 chr ENSMUST00000156068 l18 e 8 nr 2000000 chr ENSMUST00000124268 l18 e 8 nr 2500000 chr ENSMUST00000083378 l18 e 8 nr 3000000 chr ENSMUST00000169778 l18 e 8 nr 3500000 chr ENSMUST00000138098 l18 e 8 nr 4000000 chr ENSMUST00000156358 l18 e 8 nr 4500000 chr ENSMUST00000130058 l18 e 8 nr 5000000 chr ENSMUST00000031618 l18 e 8 nr 5500000 chr ENSMUST00000163848 l18 e 8 nr 6000000 chr ENSMUST00000135768 l18 e 8 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1364520 reads mapping to 655404 Unique genomic coordinates Making up 13999 groups Consisting of 6890 clusters Running PARalyzer v1.1 Parsing bowtie file(s)...nr 500000 chr ENSMUST00000163009 l18 e 9 nr 1000000 chr ENSMUST00000135969 l18 e 9 nr 1500000 chr ENSMUST00000164699 l18 e 9 nr 2000000 chr ENSMUST00000156089 l18 e 9 nr 2500000 chr ENSMUST00000162109 l18 e 9 nr 3000000 chr ENSMUST00000123719 l18 e 9 nr 3500000 chr ENSMUST00000127939 l18 e 9 nr 4000000 chr ENSMUST00000132609 l18 e 9 nr 4500000 chr ENSMUST00000137789 l18 e 9 nr 5000000 chr ENSMUST00000123109 l18 e 9 nr 5500000 chr ENSMUST00000074819 l18 e 9 Done Creating Read Groups & Clusters...Done Sorting Groups...Done Generating Output...Done! I identified a total of 1572866 reads mapping to 653105 Unique genomic coordinates Making up 14089 groups Consisting of 6955 clusters