../scripts/annotate.pl -g ../files/gencode.v11.annotation.gtf -p ../scripts/annotationRank.txt -r ../files/mm9_rmsk.bed.gz -s ../files/mm9_rmsk_info -strict -oi test.attr > test.readcsv
../scripts/annotate.pl -g ../files/gencode.v11.annotation.gtf -p ../scripts/annotationRank.txt -r ../files/mm9_rmsk.bed.gz -s ../files/mm9_rmsk_info -strict -oi test.clusters | ../scripts/PARclusters2bed.py > test.clusterbed
../scripts/annotate.pl -g ../files/gencode.v11.annotation.gtf -p ../scripts/annotationRank.txt -r ../files/mm9_rmsk.bed.gz -s ../files/mm9_rmsk_info -strict -oi test.groups | ../scripts/PARclusters2bed.py > test.groupbed