diff --git a/templates/bigwig/RGCRG-ANTISENSE b/templates/bigwig/RGCRG-ANTISENSE
index abb577f..d19b3fe 100644
--- a/templates/bigwig/RGCRG-ANTISENSE
+++ b/templates/bigwig/RGCRG-ANTISENSE
@@ -3,8 +3,12 @@ samtools view -h -@ ${cpus} ${bam} | \
 awk 'BEGIN {OFS="\\t"} {if (\$1!~/^@/) {\$2=xor(\$2,0x10)}; print}' | \
 samtools view -@ ${cpus} -Sb - > tmp.bam
 
-genomeCoverageBed -strand + -split -bg -ibam tmp.bam > ${prefix}.plusRaw.bedgraph
-genomeCoverageBed -strand - -split -bg -ibam tmp.bam > ${prefix}.minusRaw.bedgraph
+genomeCoverageBed -strand + -split -bg -ibam tmp.bam \
+  | sort -k1,1 -k2,2n \
+> ${prefix}.plusRaw.bedgraph
+genomeCoverageBed -strand - -split -bg -ibam tmp.bam \
+  | sort -k1,1 -k2,2n \
+> ${prefix}.minusRaw.bedgraph
 rm tmp.bam
 bedGraphToBigWig ${prefix}.plusRaw.bedgraph ${genomeFai} ${prefix}.plusRaw.bw
-bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
\ No newline at end of file
+bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
diff --git a/templates/bigwig/RGCRG-MATE1_SENSE b/templates/bigwig/RGCRG-MATE1_SENSE
index 41013e4..5e64b80 100644
--- a/templates/bigwig/RGCRG-MATE1_SENSE
+++ b/templates/bigwig/RGCRG-MATE1_SENSE
@@ -3,8 +3,12 @@ samtools view -h -@ ${cpus} ${bam} | \
 awk 'BEGIN {OFS="\\t"} {if (\$1!~/^@/ && and(\$2,128)>0) {\$2=xor(\$2,0x10)}; print}' | \
 samtools view -@ ${cpus} -Sb - > tmp.bam
 
-genomeCoverageBed -strand + -split -bg -ibam tmp.bam > ${prefix}.plusRaw.bedgraph
-genomeCoverageBed -strand - -split -bg -ibam tmp.bam > ${prefix}.minusRaw.bedgraph
+genomeCoverageBed -strand + -split -bg -ibam tmp.bam \
+  | sort -k1,1 -k2,2n \
+> ${prefix}.plusRaw.bedgraph
+genomeCoverageBed -strand - -split -bg -ibam tmp.bam \
+  | sort -k1,1 -k2,2n \
+> ${prefix}.minusRaw.bedgraph
 rm tmp.bam
 bedGraphToBigWig ${prefix}.plusRaw.bedgraph ${genomeFai} ${prefix}.plusRaw.bw
-bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
\ No newline at end of file
+bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
diff --git a/templates/bigwig/RGCRG-MATE2_SENSE b/templates/bigwig/RGCRG-MATE2_SENSE
index 08dc74d..cd06aac 100644
--- a/templates/bigwig/RGCRG-MATE2_SENSE
+++ b/templates/bigwig/RGCRG-MATE2_SENSE
@@ -3,8 +3,12 @@ samtools view -h -@ ${cpus} ${bam} | \
 awk 'BEGIN {OFS="\\t"} {if (\$1!~/^@/ && and(\$2,64)>0) {\$2=xor(\$2,0x10)}; print}' | \
 samtools view -@ ${cpus} -Sb - > tmp.bam
 
-genomeCoverageBed -strand + -split -bg -ibam tmp.bam > ${prefix}.plusRaw.bedgraph
-genomeCoverageBed -strand - -split -bg -ibam tmp.bam > ${prefix}.minusRaw.bedgraph
+genomeCoverageBed -strand + -split -bg -ibam tmp.bam \
+  | sort -k1,1 -k2,2n \
+> ${prefix}.plusRaw.bedgraph
+genomeCoverageBed -strand - -split -bg -ibam tmp.bam \
+  | sort -k1,1 -k2,2n \
+> ${prefix}.minusRaw.bedgraph
 rm tmp.bam
 bedGraphToBigWig ${prefix}.plusRaw.bedgraph ${genomeFai} ${prefix}.plusRaw.bw
-bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
\ No newline at end of file
+bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
diff --git a/templates/bigwig/RGCRG-NONE b/templates/bigwig/RGCRG-NONE
index e0567b9..3e6cb5d 100644
--- a/templates/bigwig/RGCRG-NONE
+++ b/templates/bigwig/RGCRG-NONE
@@ -1,3 +1,5 @@
 #!/bin/bash -eu
-genomeCoverageBed -split -bg -ibam ${bam} > ${prefix}.raw.bedgraph
-bedGraphToBigWig ${prefix}.raw.bedgraph ${genomeFai} ${prefix}.raw.bw
\ No newline at end of file
+genomeCoverageBed -split -bg -ibam ${bam} \
+  | sort -k1,1 -k2,2n \
+> ${prefix}.raw.bedgraph
+bedGraphToBigWig ${prefix}.raw.bedgraph ${genomeFai} ${prefix}.raw.bw
diff --git a/templates/bigwig/RGCRG-SENSE b/templates/bigwig/RGCRG-SENSE
index cdfea57..27098ad 100644
--- a/templates/bigwig/RGCRG-SENSE
+++ b/templates/bigwig/RGCRG-SENSE
@@ -1,5 +1,9 @@
 #!/bin/bash -eu
-genomeCoverageBed -strand + -split -bg -ibam ${bam} > ${prefix}.plusRaw.bedgraph
-genomeCoverageBed -strand - -split -bg -ibam ${bam} > ${prefix}.minusRaw.bedgraph
+genomeCoverageBed -strand + -split -bg -ibam ${bam} \
+  | sort -k1,1 -k2,2n \
+> ${prefix}.plusRaw.bedgraph
+genomeCoverageBed -strand - -split -bg -ibam ${bam} \
+  | sort -k1,1 -k2,2n \
+> ${prefix}.minusRaw.bedgraph
 bedGraphToBigWig ${prefix}.plusRaw.bedgraph ${genomeFai} ${prefix}.plusRaw.bw
-bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
\ No newline at end of file
+bedGraphToBigWig ${prefix}.minusRaw.bedgraph ${genomeFai} ${prefix}.minusRaw.bw
diff --git a/templates/bigwig/STAR-ANTISENSE b/templates/bigwig/STAR-ANTISENSE
index aaf690a..c1dd42a 100644
--- a/templates/bigwig/STAR-ANTISENSE
+++ b/templates/bigwig/STAR-ANTISENSE
@@ -13,6 +13,18 @@ if [[ ${wigRefPrefix} != - ]]; then
     sed  -ni '/^${wigRefPrefix}/p' chrSizes.txt
 fi
 
+#make sure the bedGraph files are sorted before converting to bigWig
+for bedGraph in Signal/Signal.UniqueMultiple.str1.out.bg \
+                Signal/Signal.UniqueMultiple.str2.out.bg \
+                Signal/Signal.Unique.str1.out.bg \
+                Signal/Signal.Unique.str2.out.bg; do
+    if [[ ! \$( sort -C -k1,1 -k2,2n \$bedGraph ) ]]; then
+        sort -k1,1 -k2,2n \$bedGraph > \$bedGraph.sorted && \
+        mv \$bedGraph.sorted \$bedGraph
+    fi
+done
+
+
 bedGraphToBigWig Signal/Signal.UniqueMultiple.str1.out.bg \
                  chrSizes.txt \
                  ${prefix}.UniqueMultiple.minusRaw.bw 
@@ -25,4 +37,4 @@ bedGraphToBigWig Signal/Signal.Unique.str1.out.bg \
                  ${prefix}.Unique.minusRaw.bw
 bedGraphToBigWig Signal/Signal.Unique.str2.out.bg \
                  chrSizes.txt \
-                 ${prefix}.Unique.plusRaw.bw
\ No newline at end of file
+                 ${prefix}.Unique.plusRaw.bw
diff --git a/templates/bigwig/STAR-MATE1_SENSE b/templates/bigwig/STAR-MATE1_SENSE
index b7cbe37..92e45ef 100644
--- a/templates/bigwig/STAR-MATE1_SENSE
+++ b/templates/bigwig/STAR-MATE1_SENSE
@@ -13,6 +13,18 @@ if [[ ${wigRefPrefix} != - ]]; then
     sed  -ni '/^${wigRefPrefix}/p' chrSizes.txt
 fi
 
+#make sure the bedGraph files are sorted before converting to bigWig
+for bedGraph in Signal/Signal.UniqueMultiple.str1.out.bg \
+                Signal/Signal.UniqueMultiple.str2.out.bg \
+                Signal/Signal.Unique.str1.out.bg \
+                Signal/Signal.Unique.str2.out.bg; do
+    if [[ ! \$( sort -C -k1,1 -k2,2n \$bedGraph ) ]]; then
+        sort -k1,1 -k2,2n \$bedGraph > \$bedGraph.sorted && \
+        mv \$bedGraph.sorted \$bedGraph
+    fi
+done
+
+
 bedGraphToBigWig Signal/Signal.UniqueMultiple.str1.out.bg \
                  chrSizes.txt \
                  ${prefix}.UniqueMultiple.plusRaw.bw 
@@ -25,4 +37,4 @@ bedGraphToBigWig Signal/Signal.Unique.str1.out.bg \
                  ${prefix}.Unique.plusRaw.bw
 bedGraphToBigWig Signal/Signal.Unique.str2.out.bg \
                  chrSizes.txt \
-                 ${prefix}.Unique.minusRaw.bw
\ No newline at end of file
+                 ${prefix}.Unique.minusRaw.bw
diff --git a/templates/bigwig/STAR-MATE2_SENSE b/templates/bigwig/STAR-MATE2_SENSE
index aaf690a..c1dd42a 100644
--- a/templates/bigwig/STAR-MATE2_SENSE
+++ b/templates/bigwig/STAR-MATE2_SENSE
@@ -13,6 +13,18 @@ if [[ ${wigRefPrefix} != - ]]; then
     sed  -ni '/^${wigRefPrefix}/p' chrSizes.txt
 fi
 
+#make sure the bedGraph files are sorted before converting to bigWig
+for bedGraph in Signal/Signal.UniqueMultiple.str1.out.bg \
+                Signal/Signal.UniqueMultiple.str2.out.bg \
+                Signal/Signal.Unique.str1.out.bg \
+                Signal/Signal.Unique.str2.out.bg; do
+    if [[ ! \$( sort -C -k1,1 -k2,2n \$bedGraph ) ]]; then
+        sort -k1,1 -k2,2n \$bedGraph > \$bedGraph.sorted && \
+        mv \$bedGraph.sorted \$bedGraph
+    fi
+done
+
+
 bedGraphToBigWig Signal/Signal.UniqueMultiple.str1.out.bg \
                  chrSizes.txt \
                  ${prefix}.UniqueMultiple.minusRaw.bw 
@@ -25,4 +37,4 @@ bedGraphToBigWig Signal/Signal.Unique.str1.out.bg \
                  ${prefix}.Unique.minusRaw.bw
 bedGraphToBigWig Signal/Signal.Unique.str2.out.bg \
                  chrSizes.txt \
-                 ${prefix}.Unique.plusRaw.bw
\ No newline at end of file
+                 ${prefix}.Unique.plusRaw.bw
diff --git a/templates/bigwig/STAR-NONE b/templates/bigwig/STAR-NONE
index c24d64c..5e757a0 100644
--- a/templates/bigwig/STAR-NONE
+++ b/templates/bigwig/STAR-NONE
@@ -13,10 +13,19 @@ if [[ ${wigRefPrefix} != - ]]; then
     sed  -ni '/^${wigRefPrefix}/p' chrSizes.txt
 fi
 
+#make sure the bedGraph files are sorted before converting to bigWig
+for bedGraph in Signal/Signal.UniqueMultiple.str1.out.bg \
+                Signal/Signal.Unique.str1.out.bg; do
+    if [[ ! \$( sort -C -k1,1 -k2,2n \$bedGraph ) ]]; then
+        sort -k1,1 -k2,2n \$bedGraph > \$bedGraph.sorted && \
+        mv \$bedGraph.sorted \$bedGraph
+    fi
+done
+
 bedGraphToBigWig Signal/Signal.UniqueMultiple.str1.out.bg \
                  chrSizes.txt \
                  ${prefix}.UniqueMultiple.raw.bw 
 
 bedGraphToBigWig Signal/Signal.Unique.str1.out.bg \
                  chrSizes.txt \
-                 ${prefix}.Unique.raw.bw
\ No newline at end of file
+                 ${prefix}.Unique.raw.bw
diff --git a/templates/bigwig/STAR-SENSE b/templates/bigwig/STAR-SENSE
index b7cbe37..b4c3612 100644
--- a/templates/bigwig/STAR-SENSE
+++ b/templates/bigwig/STAR-SENSE
@@ -13,6 +13,17 @@ if [[ ${wigRefPrefix} != - ]]; then
     sed  -ni '/^${wigRefPrefix}/p' chrSizes.txt
 fi
 
+#make sure the bedGraph files are sorted before converting to bigWig
+for bedGraph in Signal/Signal.UniqueMultiple.str1.out.bg \
+                Signal/Signal.UniqueMultiple.str2.out.bg \
+                Signal/Signal.Unique.str1.out.bg \
+                Signal/Signal.Unique.str2.out.bg; do
+    if [[ ! \$( sort -C -k1,1 -k2,2n \$bedGraph ) ]]; then
+        sort -k1,1 -k2,2n \$bedGraph > \$bedGraph.sorted && \
+        mv \$bedGraph.sorted \$bedGraph
+    fi
+done
+
 bedGraphToBigWig Signal/Signal.UniqueMultiple.str1.out.bg \
                  chrSizes.txt \
                  ${prefix}.UniqueMultiple.plusRaw.bw 
@@ -25,4 +36,4 @@ bedGraphToBigWig Signal/Signal.Unique.str1.out.bg \
                  ${prefix}.Unique.plusRaw.bw
 bedGraphToBigWig Signal/Signal.Unique.str2.out.bg \
                  chrSizes.txt \
-                 ${prefix}.Unique.minusRaw.bw
\ No newline at end of file
+                 ${prefix}.Unique.minusRaw.bw