diff --git a/workflow/scripts/pool_and_psuedoreplicate.py b/workflow/scripts/pool_and_psuedoreplicate.py
index 5ed1360c691a377b280d5e08b4f0415980e12ed4..f8334d058082b38af8afbacc37b76086d7325cd4 100644
--- a/workflow/scripts/pool_and_psuedoreplicate.py
+++ b/workflow/scripts/pool_and_psuedoreplicate.py
@@ -213,6 +213,9 @@ def main():
             replicate = rep + 1
             design_new_df.loc[replicate, 'tag_align'] = path_to_file
 
+        # Drop index column
+        design_new_df.drop(labels='index', axis=1, inplace=True)
+
     else:
         # Make pool of replicates
         replicate_files = design_df.tag_align.unique()