diff --git a/seqnado/config.py b/seqnado/config.py
index bebea960..436d5084 100755
--- a/seqnado/config.py
+++ b/seqnado/config.py
@@ -325,7 +325,7 @@ def setup_configuration(assay, template_data, seqnado_version):
 
 featurecounts:
     threads: 16
-    options: --primary --ignoreDup
+    options:  -p --countReadPairs
     
 """
 
diff --git a/tests/test_pipelines.py b/tests/test_pipelines.py
index 64ae1e27..fd86edff 100755
--- a/tests/test_pipelines.py
+++ b/tests/test_pipelines.py
@@ -260,7 +260,7 @@ def user_inputs(test_data_path, assay, assay_type, plot_bed):
         "make_heatmaps": "yes",
         "call_peaks": "yes",
         "peak_calling_method": "lanceotron",
-        "consensus_counts": "no",
+        "consensus_counts": "yes",
     }
 
     defaults_chip = {
@@ -271,7 +271,7 @@ def user_inputs(test_data_path, assay, assay_type, plot_bed):
         "make_heatmaps": "yes",
         "call_peaks": "yes",
         "peak_calling_method": "lanceotron",
-        "consensus_counts": "yes",
+        "consensus_counts": "no",
     }
 
     defaults_chip_rx = {
@@ -409,7 +409,7 @@ def design(seqnado_run_dir, assay_type, assay):
     completed = subprocess.run(" ".join(cmd), shell=True, cwd=seqnado_run_dir)
     assert completed.returncode == 0
 
-    if assay == "chip":
+    if assay == "chip" or assay == "atac":
         # Add merge column to design file
         import pandas as pd