diff --git a/coolpuppy/__main__.py b/coolpuppy/__main__.py
index 99f54f4..b42e2bf 100644
--- a/coolpuppy/__main__.py
+++ b/coolpuppy/__main__.py
@@ -532,9 +532,10 @@ def _excepthook(exc_type, value, tb):
                 json.dump(outdict, fp)  # , sort_keys=True, indent=4)
                 logging.info(f"Saved individual pileups to {json_path}")
     else:
-        pup = PU.pileupsWithControl(nproc)
+        pup, n = PU.pileupsWithControl(nproc)
         headerdict = vars(args)
         headerdict['resolution'] = int(c.binsize)
+        headerdict['n'] = int(n)
         try:
             save_array_with_header(pup, headerdict, os.path.join(args.outdir, outname))
         except FileNotFoundError:
diff --git a/coolpuppy/coolpup.py b/coolpuppy/coolpup.py
index f0b1472..1956a98 100644
--- a/coolpuppy/coolpup.py
+++ b/coolpuppy/coolpup.py
@@ -1160,6 +1160,7 @@ def pileupsWithControl(self, nproc=1):
         loops, nums, cov_starts, cov_ends, ns = list(zip(*mymap(f, self.chroms)))
         loop = np.sum(loops, axis=0)
         n = np.sum(ns)
+        n_return = n
         num = np.sum(nums, axis=0)
         if self.coverage_norm:
             cov_start = np.sum(cov_starts, axis=0)
@@ -1191,7 +1192,7 @@ def pileupsWithControl(self, nproc=1):
         if nproc > 1:
             p.close()
         loop[~np.isfinite(loop)] = 0
-        return loop
+        return loop, n_return
 
     def pileupsByWindow(
         self, chrom, expected=False, ctrl=False,