# variables for small RNA pipeline intersecting
	#MASK=$COMMON_FOLDER/AGPv4.tRNA+rRNA.bed # tRNA, rRNA, nonCoding RNA (flyBase) from UCSC table browser

	#tRNA=$COMMON_FOLDER/tn1.tRNA.bed
	rRNA=$COMMON_FOLDER/tn1.rRNA.bed
	#rRNA=$COMMON_FOLDER/AGPv4.rDNA.repeatMasker.bed # run repeatMasker using rDNA sequence
	##RM_rRNA=$COMMON_FOLDER/AGPv4.repBase.repeatMasker.rRNA.bed.gz # run repeatMasker using repBase default and extract the ones classified as rRNA

	piRNA_Cluster=$COMMON_FOLDER/tn1.piRNAcluster.bed

	##repeatMasker=$COMMON_FOLDER/AGPv4.repeatMasker.bed #from ncbi 

	Trn=$COMMON_FOLDER/tn1.transposon.bed 

	Genes=$COMMON_FOLDER/tn1.genes.bed # = gene
	#Exons=$COMMON_FOLDER/UCSC.refSeq.exon.bed.gz # = exons
	#Introns=$COMMON_FOLDER/UCSC.refSeq.intron.bed.gz # = introns
	#FiveUTR=$COMMON_FOLDER/UCSC.refSeq.5UTR.bed.gz # = 5' UTR
	#CDS=$COMMON_FOLDER/UCSC.refSeq.CDS.bed.gz # = CDS
	#ThreeUTR=$COMMON_FOLDER/UCSC.refSeq.3UTR.bed.gz # = 3' UTR
	#cisNATs=$COMMON_FOLDER/cisNATs.bed.gz # cis-NATs
	#structural_loci=$COMMON_FOLDER/structured_loci.bed.gz # structural loci
	#lincRNA=$COMMON_FOLDER/lincRNA.Young.bed6.gz # linc RNA identified in 'Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol Evol. 2012;4(4):427-42.'
	## unannotated=$COMMON_FOLDER/unannotated_genome.bed.gz #may be able to generate this myself

	declare -a TARGETS=( \
	"tRNA" \
	"rRNA" \
	"piRNA_Cluster" \
	"repeatMasker" \
	"Genes" \
	"Exons" \
	"Introns" \
	"FiveUTR" \
	"CDS" \
	"ThreeUTR" \
	"cisNATs" \
	"structural_loci" \
	"lincRNA" \
 	)

	declare -a TARGETS_SHORT=( \
	"piRNA_Cluster" \
	"repeatMasker" \
	"Genes" \
	"Exons" \
	"Introns" \
	"FiveUTR" \
	"CDS" \
	"ThreeUTR" \
 	)

	declare -a TARGETS_EXCLUSIVE=(\
	"piRNA_Cluster" \
	"CDS" \
	"FiveUTR" \
	"ThreeUTR" \
	"Introns" \
	"repeatMasker" \
	)

# variables for small RNA direct mapping
	#declare -a DIRECT_MAPPING=( "transposon" "tRNA" "genes" ) # need to have BowtieIndex/repBase # BowtieIndex/piRNAcluster
	declare -a DIRECT_MAPPING=( "transposon" "piRNAcluster" )

# gtf files for rnaseq/deg/cage htseq-count
	# Genes_transposon_Cluster=$COMMON_FOLDER/AGPv4.genes+transposon+piRNACluster.gtf
	# Genes_repBase_Cluster=$COMMON_FOLDER/AGPv4.genes+repBase+piRNACluster.gtf
	declare -a HTSEQ_TARGETS=( "Genes_transposon_Cluster" "Genes_repBase_Cluster" )