rmsk	/bar/nshah/reference/rnapipelinerefhg38/rmskhg38.bed6.gz
rmskannotationfile	/bar/nshah/reference/rnapipelinerefhg38/repeatmasker_description_uniq.lst
gencodeplusdic	/bar/nshah/reference/rnapipelinerefhg38/genecode_plus_hg38.dic
gencodeminusdic	/bar/nshah/reference/rnapipelinerefhg38/genecode_minus_hg38.dic
focusgenes	/bar/nshah/reference/rnapipelinerefhg38/oncogenes_augmented.txt
plusintron	/bar/nshah/reference/rnapipelinerefhg38/gencode.v25.annotation.sorted.gtf_introns_plus_sorted.gz
minusintron	/bar/nshah/reference/rnapipelinerefhg38/gencode.v25.annotation.sorted.gtf_introns_minus_sorted.gz
