diff --git a/deeptools/computeMatrix.py b/deeptools/computeMatrix.py
index 62a95657..02cc1fd4 100644
--- a/deeptools/computeMatrix.py
+++ b/deeptools/computeMatrix.py
@@ -355,6 +355,14 @@ def process_args(args=None):
     if args.quiet is True:
         args.verbose = False
 
+    # Ensure before and after region length is positive
+    if args.beforeRegionStartLength < 0:
+        print(f"beforeRegionStartLength changed from {args.beforeRegionStartLength} into {abs(args.beforeRegionStartLength)}")
+        args.beforeRegionStartLength = abs(args.beforeRegionStartLength)
+    if args.afterRegionStartLength < 0:
+        print(f"afterRegionStartLength changed from {args.afterRegionStartLength} into {abs(args.afterRegionStartLength)}")
+        args.afterRegionStartLength = abs(args.afterRegionStartLength)
+
     if args.command == 'scale-regions':
         args.nanAfterEnd = False
         args.referencePoint = None