diff --git a/code/replace_with_tab b/code/replace_with_tab
new file mode 100755
index 0000000..71aa7b0
--- /dev/null
+++ b/code/replace_with_tab
@@ -0,0 +1,13 @@
+#!/bin/tcsh -f
+
+##
+## USAGE: replace_tab STRING
+##
+
+if ($#argv != 1) then
+  usage $0
+  exit
+endif
+
+sed "s/$1/	/"
+
diff --git a/inputs/params.bash b/inputs/params.bash
index a72cff2..eb920cc 100755
--- a/inputs/params.bash
+++ b/inputs/params.bash
@@ -24,6 +24,7 @@ class_code="iusx"
 min_length="200"
 extend_TSS="1500"
 ref_annot_bed=$protein_coding_bed
+excluding_region="../referenceFiles/excluding_region.bed"
 
 ##################
 # 4. whole_assembly
@@ -45,7 +46,7 @@ CPAT_cutoff="../referenceFiles/CPAT_Reference/Human_cutoff.txt"
 ##################
 # 6. annotate
 #    <all annotation bed files in double quote>
-other_annotations="../referenceFiles/RefSeqRefFlat.bed ../referenceFiles/Homo_sapiens.GRCh37.79.bed"
+other_annotations="../referenceFiles/RefSeqRefFlat.bed ../referenceFiles/Homo_sapiens.GRCh37.75.bed"
 
 ##################
 # 6. summarize + split_table
diff --git a/run.bash b/run.bash
index ab56925..b688eed 100755
--- a/run.bash
+++ b/run.bash
@@ -25,7 +25,7 @@ code/wait_jobs.bash cuffmerge
 cd ..
 
 cd identify
-code/identify.bash $class_code $min_length $extend_TSS $ref_annot_bed $ref_annot_gtf ../cuffmerge/merged.gtf
+code/identify.bash $class_code $min_length $extend_TSS $ref_annot_bed $ref_annot_gtf $excluding_region ../cuffmerge/merged.gtf
 cd ..
 
 cd whole_assembly