# variables for small RNA pipeline intersecting
	MASK=$COMMON_FOLDER/dm6.tRNA+rRNA.bed.gz # tRNA, rRNA, nonCoding RNA (flyBase) from UCSC table browser

	tRNA=$COMMON_FOLDER/dm6.tRNA.bed.gz
	rRNA=$COMMON_FOLDER/dm6.rDNA.repeatMasker.bed.gz # run repeatMasker using rDNA sequence
	RM_rRNA=$COMMON_FOLDER/dm6.repBase.repeatMasker.rRNA.bed.gz # run repeatMasker using repBase default and extract the ones classified as rRNA

	piRNA_Cluster=$COMMON_FOLDER/dm6.piRNAcluster.bed.gz
	# piRNA_Cluster_42AB=$COMMON_FOLDER/Brennecke.piRNAcluster.42AB.bed6 # 42AB
	# piRNA_Cluster_20A=$COMMON_FOLDER/Brennecke.piRNAcluster.20A.bed6 # 20A
	# piRNA_Cluster_flam=$COMMON_FOLDER/Brennecke.piRNAcluster.flam.bed6 # flam

	repeatMasker=$COMMON_FOLDER/dm6.repBase.repeatMasker.bed.gz # generate by RepeatMasker -pa 8 -s -low -species drosophila -gff dm6.fa
	RM_ARTEFACT=$COMMON_FOLDER/dm6.repBase.repeatMasker.ARTEFACT.bed.gz
	RM_DNA=$COMMON_FOLDER/dm6.repBase.repeatMasker.DNA.bed.gz
	RM_LINE=$COMMON_FOLDER/dm6.repBase.repeatMasker.LINE.bed.gz
	RM_Low_complexity=$COMMON_FOLDER/dm6.repBase.repeatMasker.Low_complexity.bed.gz
	RM_LTR=$COMMON_FOLDER/dm6.repBase.repeatMasker.LTR.bed.gz
	RM_Other=$COMMON_FOLDER/dm6.repBase.repeatMasker.Other.bed.gz
	RM_RC=$COMMON_FOLDER/dm6.repBase.repeatMasker.RC.bed.gz
	RM_RNA=$COMMON_FOLDER/dm6.repBase.repeatMasker.RNA.bed.gz
	RM_Satellite=$COMMON_FOLDER/dm6.repBase.repeatMasker.Satellite.bed.gz
	RM_Simple_repeat=$COMMON_FOLDER/dm6.repBase.repeatMasker.Simple_repeat.bed.gz
	RM_Unknown=$COMMON_FOLDER/dm6.repBase.repeatMasker.Unknown.bed.gz

	# Trn=$COMMON_FOLDER/Zamore.transposon.bed.gz # transposon region used in Li, et al., Cell, 2009. More conserved than repeat masker
	# Trn_GROUP0=$COMMON_FOLDER/Zamore.transposon.group0.bed.gz # transposons that failed to pass threshold in Li, et al., Cell, 2009. More conserved than repeat masker
	# Trn_GROUP1=$COMMON_FOLDER/Zamore.transposon.group1.bed.gz # group 1 transposon in Li, et al., Cell, 2009, mainly germline
	# Trn_GROUP2=$COMMON_FOLDER/Zamore.transposon.group2.bed.gz # group 2 transposon in Li, et al., Cell, 2009
	# Trn_GROUP3=$COMMON_FOLDER/Zamore.transposon.group3.bed.gz # group 3 transposon in Li, et al., Cell, 2009, mainly somatic
	Genes=$COMMON_FOLDER/UCSC.refSeq.gene.bed12.gz # = 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
	declare -a TARGETS=( \
	"piRNA_Cluster" \
	"repeatMasker" "RM_DNA" "RM_LINE" "RM_LTR" "RM_RNA" "RM_Satellite" \
	"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=( "repBase" "piRNAcluster" "tRNA" ) # need to have BowtieIndex/repBase # BowtieIndex/piRNAcluster

# gtf files for rnaseq/deg/cage htseq-count
	# Genes_transposon_Cluster=$COMMON_FOLDER/
	# Genes_repBase_Cluster=$COMMON_FOLDER/
	declare -a HTSEQ_TARGETS=( "" )