diff --git a/R/utils.R b/R/utils.R
index 15ce011..ddc72fa 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -34,8 +34,8 @@ filterEmptyChr <- function(gr){
 ####################################
 ##### FUNCTION GET SEQINFO ######
 ####################################
-getSeqInfo <- function(genomeBuild = "hg19", genomeStyle = "NCBI"){
-	bsg <- paste0("BSgenome.Hsapiens.UCSC.", genomeBuild)
+getSeqInfo <- function(genomeSpecies = "Hsapiens", genomeBuild = "hg19", genomeStyle = "NCBI"){
+	bsg <- paste0("BSgenome.", genomeSpecies, ".", genomeStyle, ".", genomeBuild)
 	if (!require(bsg, character.only=TRUE, quietly=TRUE, warn.conflicts=FALSE)) {
 		seqinfo <- Seqinfo(genome=genomeBuild)
 	} else {
diff --git a/scripts/createPanelOfNormals.R b/scripts/createPanelOfNormals.R
index 6a7123f..41c6e17 100644
--- a/scripts/createPanelOfNormals.R
+++ b/scripts/createPanelOfNormals.R
@@ -17,7 +17,8 @@ option_list <- list(
 	make_option(c("--chrNormalize"), type="character", default="c(1:22)", help = "Specify chromosomes to normalize GC/mappability biases"),
 	make_option(c("--maleChrXLogRThres"), type="numeric", default=-0.80, help = "ChrX Log ratio threshold to confirm as male gender."),
 	make_option(c("-e", "--exons.bed"), type = "character", default=NULL, help = "Path to bed file containing exon regions."),
-	make_option(c("--method"), type = "character", default="median", help="Median or Mean.")
+	make_option(c("--method"), type = "character", default="median", help="Median or Mean."),
+	make_option(c("--normalizeX"), type="logical", default=TRUE, help = "Normalize chrX by median. Default: [%default]")
 	#make_option(c("--ylim"), type = "character", default="c(-2,2)", help="Y-limits for plotting of mean/median log ratios")
 )
 parseobj <- OptionParser(option_list=option_list)
@@ -35,6 +36,7 @@ outfile <- opt$outfile
 genomeStyle <- opt$genomeStyle
 #ylim <- eval(parse(text = opt$ylim))
 maleChrXLogRThres <- opt$maleChrXLogRThres
+normalizeX <- as.logical(opt$normalizeX)
 chrs <- as.character(eval(parse(text = opt$chrs)))
 chrNormalize <- as.character(eval(parse(text=opt$chrNormalize))); 
 seqlevelsStyle(chrs) <- genomeStyle
@@ -94,8 +96,9 @@ for (i in 1:length(files)){
 	chrXStr <- grep("X", chrs, value = TRUE)
 	chrXInd <- as.character(seqnames(normalGR)) == chrXStr
 	## Normalize chrX ##
-	values(normalGR)[[sid]][chrXInd] <- values(normalGR)[[sid]][chrXInd] - chrXMedian
-	
+	if (normalizeX){
+	  values(normalGR)[[sid]][chrXInd] <- values(normalGR)[[sid]][chrXInd] - chrXMedian
+	}
 }
 
 
diff --git a/scripts/runIchorCNA.R b/scripts/runIchorCNA.R
index 376dab2..036f552 100644
--- a/scripts/runIchorCNA.R
+++ b/scripts/runIchorCNA.R
@@ -45,6 +45,7 @@ option_list <- list(
   make_option(c("--chrs"), type="character", default="c(1:22,\"X\")", help = "Specify chromosomes to analyze. Default: [%default]"),
   make_option(c("--genomeBuild"), type="character", default="hg19", help="Geome build. Default: [%default]"),
   make_option(c("--genomeStyle"), type = "character", default = "NCBI", help = "NCBI or UCSC chromosome naming convention; use UCSC if desired output is to have \"chr\" string. [Default: %default]"),
+  make_option(c("--genomeSpecies"), type="character", default="Hsapiens", help="Geome species. Default: [%default]"),
   make_option(c("--normalizeMaleX"), type="logical", default=TRUE, help = "If male, then normalize chrX by median. Default: [%default]"),
   make_option(c("--minTumFracToCorrect"), type="numeric", default=0.1, help = "Tumor-fraction correction of bin and segment-level CNA if sample has minimum estimated tumor fraction. [Default: %default]"), 
   make_option(c("--fracReadsInChrYForMale"), type="numeric", default=0.001, help = "Threshold for fraction of reads in chrY to assign as male. Default: [%default]"),
@@ -106,6 +107,7 @@ gender <- NULL
 outImage <- paste0(outDir,"/", patientID,".RData")
 genomeBuild <- opt$genomeBuild
 genomeStyle <- opt$genomeStyle
+genomeSpecies <- opt$genomeSpecies
 chrs <- as.character(eval(parse(text = opt$chrs)))
 chrTrain <- as.character(eval(parse(text=opt$chrTrain))); 
 chrNormalize <- as.character(eval(parse(text=opt$chrNormalize))); 
@@ -125,7 +127,7 @@ if (!is.null(libdir) && libdir != "None"){
 }
 
 ## load seqinfo 
-seqinfo <- getSeqInfo(genomeBuild, genomeStyle)
+seqinfo <- getSeqInfo(genomeSpecies, genomeBuild, genomeStyle)
 
 if (substr(tumour_file,nchar(tumour_file)-2,nchar(tumour_file)) == "wig") {
   wigFiles <- data.frame(cbind(patientID, tumour_file))