Merge remote-tracking branch 'upstream/activeDev' into activeDev

CCBR · Sep 5, 2019 · e69aec2 · e69aec2
2 parents e3b3407 + d4159d6
commit e69aec2
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Showing 36 changed files with 209 additions and 117 deletions.
diff --git a/Mmul_8.0.1.json b/Mmul_8.0.1.json
@@ -5,7 +5,7 @@
  		"rnaseq": {
  			"GENOMEFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/ref.fa",
  			"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/genes.gtf",
- 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/STAR/2.5.2b/genes-",
+ 			"STARDIR": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/STAR/2.7.0f/genes-",
 			"QUALIMAP_INFO": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/qualimap_info.txt",
                         "KARYOPLOTER": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/karyoplot_gene_coordinates.txt",
  			"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/annotate.genes.txt",
@@ -17,7 +17,7 @@
  			"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/rsemref/Mmul_8.0.1",
  			"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/Mmul_8.0.1.rRNA_interval_list",
  			"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
- 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/STAR/2.5.2b/genes-",
+ 			"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/STAR/2.7.0f/genes-",
  			"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
  			"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/Indices/Mmul_8.0.1_basic/ref.fa",
  			"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
@@ -29,5 +29,3 @@
  		"ChIPseq": {}
 	}
 }
-
-
diff --git a/Results-template/Scripts/Deseq2Report.Rmd b/Results-template/Scripts/Deseq2Report.Rmd
@@ -319,7 +319,7 @@ for(i in seq(1, length(contras), by = 2)) {
     write.table(deseq2out,file=paste("DESeq2_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt",sep=""),row.names=FALSE,col.names=TRUE,quote=FALSE,sep="\t")
     
     ## Pathway enrichment analysis
-    if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38") {
+    if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38" | SPECIES=="hg38_30") {
       iup=which(final$pvalue<0.05 & final$FoldChange >=0)
       idw=which(final$pvalue<0.05 & final$FoldChange <0)
       fin.up=final[iup,]
@@ -341,7 +341,7 @@ for(i in seq(1, length(contras), by = 2)) {
     gdw=apply(array(as.character(x2)),1,function(z) unlist(strsplit(z, "\\|"))[2])
     extension=paste0("_",contras[i],"_vs_",contras[i+1],".txt")
 
-      if (SPECIES=="hg19" | SPECIES=="hg38") {
+      if (SPECIES=="hg19" | SPECIES=="hg38"| SPECIES=="hg38_30") {
         write.table(gup,paste0("DESeq2_gene_up_path",extension),quote=F,row.names=F,col.names=F)
         write.table(gdw,paste0("DESeq2_gene_dw_path",extension),quote=F,row.names=F,col.names=F)
       } 
@@ -403,14 +403,14 @@ for(i in seq(1, length(contras), by = 2)) {
     volcano_data=as.data.frame(cbind(gene,log_FC,log_pval,Significant))
     v_fdr[[i]] <- plot_ly(data = volcano_data, x = log_FC, y = log_pval, text = gene, mode = "markers", color = Significant) %>% layout(title =paste(contras[i]," vs. ",contras[i+1],sep=""),xaxis=list(title="Fold Change",range =c(-5,5),tickvals=c(-5,-4,-3,-2,-1,0,1,2,3,4,5),ticktext=c('-32','-16','-8','-4','-2','1','2','4','8','16','32')),yaxis=list(title="-Log10 FDR",range =c(0,15)))
 
-    if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
+    if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
       system(paste0("cd ",getwd(),"; python ../Scripts/FC2karyo.py DESeq2_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt 1 3 ",SPECIES," ",KARYOBEDS," > DESeq2_deg_",contras[i],"_vs_",contras[i+1],".input.karyo"))
       system(paste0("cd ",getwd(),"; python ../Scripts/karyoplot.py DESeq2_deg_",contras[i],"_vs_",contras[i+1],".input.karyo ",SPECIES))
       ki1=paste0("DESeq2_deg_",contras[i],"_vs_",contras[i+1],".input.karyo1.png")
       ki2=paste0("DESeq2_deg_",contras[i],"_vs_",contras[i+1],".input.karyo2.png")
     }
 
-    if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
+    if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
       system(paste0("cd ",getwd(),";/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/r_env/bin/Rscript ../Scripts/karyoploter.R -o deseq2 -d DESeq2_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt -c ", params$karyotext, " -g ", SPECIES))
     }
 }
@@ -447,7 +447,7 @@ v_fdr
 ### Page1
 
 ```{r, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
+if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
   cat("![](deseq2_karyoplot1.png)")
 } else {
   cat("Genome Not Supported")
@@ -458,7 +458,7 @@ if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECI
 ### Page2
 
 ```{r, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
+if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
   cat("![](deseq2_karyoplot2.png)")
 } else {
   cat("Genome Not Supported")
@@ -471,7 +471,7 @@ if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECI
 ### Page1
 
 ```{r, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
+if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
   cat("![](",ki1,")")
 } else {
   cat("Genome Not suporrted")
@@ -481,7 +481,7 @@ if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(gre
 ### Page2
 
 ```{r, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
+if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
   cat("![](",ki2,")")
 } else {
   cat("Genome Not Supported")
@@ -494,7 +494,7 @@ if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(gre
 ### Up-Regulated
 
 ```{r, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38"){
+if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38" | SPECIES=="hg38_30"){
   pup
 } else {
   cat("Genome Not Supported")
@@ -504,7 +504,7 @@ if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38"){
 ### Down-Regulated
 
 ```{r, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38"){
+if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38" | SPECIES=="hg38_30"){
   pdw
 } else {
   cat("Genome Not Supported")

diff --git a/Results-template/Scripts/EdgerReport.Rmd b/Results-template/Scripts/EdgerReport.Rmd
@@ -370,7 +370,7 @@ for(i in 1:nb){
   extension=paste0("_",cons[i],".txt")
 
   ## Pathway enrichment analysis (Over-representation test ~ l2p)
-  if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38") {
+  if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38" | SPECIES=="hg38_30") {
     iup=which(final$PValue<0.05 & final$FC >=0)
     idw=which(final$PValue<0.05 & final$FC <0)
     fin.up=final[iup,]
@@ -393,7 +393,7 @@ for(i in 1:nb){
     x2=rownames(fin.dw)
     gdw=apply(array(as.character(x2)),1,function(z) unlist(strsplit(z, "\\|"))[2])
     
-    if (SPECIES=="hg19" | SPECIES=="hg38") {
+    if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30") {
       write.table(gup,paste0("edgeR_gene_up_path",extension),quote=F,row.names=F,col.names=F)
       write.table(gdw,paste0("edgeR_gene_dw_path",extension),quote=F,row.names=F,col.names=F)
     }
@@ -460,14 +460,14 @@ for(i in 1:nb){
   volcano_data=as.data.frame(cbind(gene,log_FC,log_pval,Significant))
   v_fdr[[i]] <- plot_ly(data = volcano_data, x = log_FC, y = log_pval, text = gene, mode = "markers", color = Significant) %>% layout(title =paste(contras[i]," vs. ",contras[i+1],sep=""),xaxis=list(title="Fold Change",range =c(-5,5),tickvals=c(-5,-4,-3,-2,-1,0,1,2,3,4,5),ticktext=c('-32','-16','-8','-4','-2','1','2','4','8','16','32')),yaxis=list(title="-Log10 FDR",range =c(0,15)))
 
-  if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))) {    
+  if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))) {    
     system(paste0("cd ",getwd(),"; python ../Scripts/FC2karyo.py edgeR_DEG_",cons[i],"_all_genes.txt 1 3 ",SPECIES," ",KARYOBEDS," > edgeR_DEG_",cons[i],".input.karyo"))
     system(paste0("cd ",getwd(),"; python ../Scripts/karyoplot.py edgeR_DEG_",cons[i],".input.karyo ",SPECIES))
     ki1=paste0("edgeR_DEG_",cons[i],".input.karyo1.png")
     ki2=paste0("edgeR_DEG_",cons[i],".input.karyo2.png")
   }
 
-  if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ) {
+  if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ) {
     system(paste0("cd ",getwd(),";/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/r_env/bin/Rscript ../Scripts/karyoploter.R -o edgeR -d edgeR_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt -c ", params$karyotext, " -g ", SPECIES))
   }
 }
@@ -505,7 +505,7 @@ v_fdr
 ### Page1
 
 ```{r de_karyo1, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
+if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
   cat("![](edgeR_karyoplot1.png)")
 } else {
   cat("Genome Not Supported")
@@ -516,7 +516,7 @@ if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECI
 ### Page2
 
 ```{r de_karyo2, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
+if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
   cat("![](edgeR_karyoplot2.png)")
 } else {
   cat("Genome Not Supported")
@@ -529,7 +529,7 @@ if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECI
 ### Page1
 
 ```{r bin_karyo1, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
+if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
   cat("![](",ki1,")")
 } else {
   cat("Genome Not suporrted")
@@ -539,7 +539,7 @@ if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(gre
 ### Page2
 
 ```{r bin_karyo2, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
+if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
   cat("![](",ki2,")")
 } else {
   cat("Genome Not Supported")
@@ -551,7 +551,7 @@ if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(gre
 ### Up-Regulated
 
 ```{r up_l2p, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38"){
+if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38" | SPECIES=="hg38_30"){
   pup
 } else {
   cat("Genome Not Supported")
@@ -561,7 +561,7 @@ if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38"){
 ### Down-Regulated
 
 ```{r down_l2p, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38"){
+if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38" | SPECIES=="hg38_30"){
   pdw
 } else {
   cat("Genome Not Supported")

diff --git a/Results-template/Scripts/LimmaReport.Rmd b/Results-template/Scripts/LimmaReport.Rmd
@@ -317,7 +317,7 @@ for (i in 1:nb) {
   mpval=cbind(mpval,final$P.Value)
   
   ## Pathway enrichment analysis (Over-representation test ~ l2p)
-  if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38") {
+  if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38" | SPECIES=="hg38_30") {
     
     iup=which(final$P.Value<0.05 & final$FC >=0)
     idw=which(final$P.Value<0.05 & final$FC <0)
@@ -342,7 +342,7 @@ for (i in 1:nb) {
     
     extension=paste0("_",cons[i],".txt")
 
-    if (SPECIES=="hg19" | SPECIES=="hg38") {
+    if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30") {
       write.table(gup,paste0("limma_gene_up_path",extension),quote=F,row.names=F,col.names=F)
       write.table(gdw,paste0("limma_gene_dw_path",extension),quote=F,row.names=F,col.names=F)
     }
@@ -426,14 +426,14 @@ for (i in 1:nb) {
   write.table(limmaout,file=paste("limma_DEG_",cons[i],"_all_genes.txt",sep=""),row.names=FALSE,col.names=TRUE,quote=FALSE,sep="\t")
   
   
-  if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))) {    
+  if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))) {    
     system(paste0("cd ",getwd(),"; python ../Scripts/FC2karyo.py limma_DEG_",cons[i],"_all_genes.txt 1 3 ",SPECIES," ",KARYOBEDS," > limma_DEG_",cons[i],".input.karyo"))
     system(paste0("cd ",getwd(),"; python ../Scripts/karyoplot.py limma_DEG_",cons[i],".input.karyo ",SPECIES))
     ki1=paste0("limma_DEG_",cons[i],".input.karyo1.png")
     ki2=paste0("limma_DEG_",cons[i],".input.karyo2.png") 
   }
   
-  if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ) {
+  if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ) {
     system(paste0("cd ",getwd(),";/data/CCBR_Pipeliner/db/PipeDB/Conda/envs/r_env/bin/Rscript ../Scripts/karyoploter.R -o limma -d limma_DEG_",contras[i],"-",contras[i+1],"_all_genes.txt -c ", params$karyotext, " -g ", SPECIES))
   }
   
@@ -472,7 +472,7 @@ v_fdr
 ### **Page1**
 
 ```{r karyo_gene1, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
+if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
   cat("![](limma_karyoplot1.png)")
 } else {
   cat("Genome Not Supported")
@@ -483,7 +483,7 @@ if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECI
 ### Page2
 
 ```{r karyo_gene2, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
+if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9" | SPECIES=="canFam3" | SPECIES=="Mmul_8.0.1" ){
   cat("![](limma_karyoplot2.png)")
 } else {
   cat("Genome Not Supported")
@@ -496,7 +496,7 @@ if (SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9" | SPECI
 ### **Page1**
 
 ```{r karyo_bin1, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
+if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
   cat("![](",ki1,")")
 } else {
   cat("Genome Not suporrted")
@@ -506,7 +506,7 @@ if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(gre
 ### Page2
 
 ```{r karyo_bin2, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
+if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="hg38_30" | SPECIES=="mm10" | SPECIES=="mm9")&&(grepl("genes",params$dtype))){
   cat("![](",ki2,")")
 } else {
   cat("Genome Not Supported")
@@ -518,7 +518,7 @@ if ((SPECIES=="hg19" | SPECIES=="hg38" | SPECIES=="mm10" | SPECIES=="mm9")&&(gre
 ### **Up-Regulated**
 
 ```{r l2p_up, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38"){
+if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38" | SPECIES=="hg38_30"){
   pup
 } else {
   cat("Genome Not Supported")
@@ -528,7 +528,7 @@ if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38"){
 ### Down-Regulated
 
 ```{r l2p_down, echo=FALSE, warning=FALSE,message=FALSE,results='asis'}
-if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38"){
+if (SPECIES=="hg19" | SPECIES=="mm10" | SPECIES=="hg38" | SPECIES=="hg38_30"){
   pdw
 } else {
   cat("Genome Not Supported")

diff --git a/Results-template/Scripts/karyoploter.R b/Results-template/Scripts/karyoploter.R
@@ -6,7 +6,7 @@ parser$add_argument("-d", "--degout", type="character", required=TRUE,
 parser$add_argument("-c", "--gene2coord", type="character", required=TRUE,
                     help="Gene to coordinate file")
 parser$add_argument("-g", "--genome", type="character", required=TRUE,
-                    help="Genome .. either hg19/hg38/mm9/mm10/Mmul8.0.1/canFam3")
+                    help="Genome .. either hg19/hg38/mm9/mm10/Mmul8.0.1/canFam3/hg38_30")
 parser$add_argument("-f", "--fdr", type="double", default=0.05,
                     help="FDR cutoff to use")
 parser$add_argument("-o", "--outfileprefix", type="character", required=TRUE,
@@ -20,8 +20,8 @@ if (! file.exists(f)) {
   stop(paste("File does not exist:",f))
 }
 
-if (! args$genome %in% c("hg19","hg38","mm9","mm10","Mmul8.0.1","canFam3")) {
-  stop("Only hg19/hg38/mm9/mm10/Mmul8.0.1/canFam3 genomes are supported!")
+if (! args$genome %in% c("hg19","hg38","hg38_30","mm9","mm10","Mmul8.0.1","canFam3")) {
+  stop("Only hg19/hg38/mm9/mm10/Mmul8.0.1/canFam3/hg38_30 genomes are supported!")
 }
 
 
@@ -54,7 +54,7 @@ if(nrow(deseqout_filtered_w_coord)==0){
 genome=args$genome
 chrs=c()
 maxchrs=0
-if (genome %in% c("hg19","hg38")) {maxchrs=22}
+if (genome %in% c("hg19","hg38","hg38_30")) {maxchrs=22}
 if (genome %in% c("mm10","mm9")) {maxchrs=19}
 if (genome %in% c("rheMac8")) {maxchrs=20}
 if (genome %in% c("canFam3")) {maxchrs=38}
@@ -96,6 +96,7 @@ if (nrow(neg_strand_down_triangle)>0) {neg_strand_down_triangle$log2fc=neg_scale
 for (i in seq(1,length(chrs_subsets))) {
   chrs2=unlist(chrs_subsets[i])
   png(paste(args$outfileprefix,"_karyoplot",i,".png",sep=""), width = 10, height = 6, units = 'in', res = 1600)
+  if (grepl('_', genome)){genome <- strsplit(genome, "_")[[1]][1]}
   kp <- plotKaryotype(genome=genome, plot.type=2, chromosomes = chrs2)
 
   kpDataBackground(kp, data.panel = 1, r0=0, r1=0.9)

diff --git a/Results-template/Scripts/make_sample_network.pl b/Results-template/Scripts/make_sample_network.pl
@@ -10,7 +10,7 @@
 my $cmd = '';
 my $vcf=shift;
 
-$cmd = 'module load vcftools; vcftools --vcf ' . $vcf . ' --plink --remove-indels --out plink';
+$cmd = 'module load vcftools; vcftools --gzvcf ' . $vcf . ' --plink --remove-indels --out plink';
 system($cmd);
 $cmd = 'module load plink/1.9.0-beta4.4; plink --file plink --distance-matrix --out distance';
 system($cmd);