diff --git a/mouse/Snakefile b/mouse/Snakefile
index 86fd5c51a10487cb4d18c5e242e81cbd079e5bea..bbb72d022c4350795265277a202ccdbcbb90fd33 100644
--- a/mouse/Snakefile
+++ b/mouse/Snakefile
@@ -421,57 +421,57 @@ rule frip:
 # Based on ENCODE `overlap_peaks.py` - recommended for histone marks.
 # Need to pool peaks first for each replicate
 
-# rule pool_peaks:
-#     input:
-#         E10 = expand(["results/macs2/{case}_vs_{control}_E10.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E11 = expand(["results/macs2/{case}_vs_{control}_E11.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E12 = expand(["results/macs2/{case}_vs_{control}_E12.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E13 = expand(["results/macs2/{case}_vs_{control}_E13.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E14 = expand(["results/macs2/{case}_vs_{control}_E14.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E15 = expand(["results/macs2/{case}_vs_{control}_E15.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK)
-#     output:
-#         E10 = expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#         E11 = expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#         E12 = expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#         E13 = expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#         E14 = expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#         E15 = expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK)
-#     run:
-#         shell("cat {input.E10} > {output.E10}")
-#         shell("cat {input.E11} > {output.E11}")
-#         shell("cat {input.E12} > {output.E12}")
-#         shell("cat {input.E13} > {output.E13}")
-#         shell("cat {input.E14} > {output.E14}")
-#         shell("cat {input.E15} > {output.E15}")
+rule pool_peaks:
+    input:
+        E10 = expand(["results/macs2/{case}_vs_{control}_E10.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E11 = expand(["results/macs2/{case}_vs_{control}_E11.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E12 = expand(["results/macs2/{case}_vs_{control}_E12.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E13 = expand(["results/macs2/{case}_vs_{control}_E13.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E14 = expand(["results/macs2/{case}_vs_{control}_E14.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E15 = expand(["results/macs2/{case}_vs_{control}_E15.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK)
+    output:
+        E10 = expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E11 = expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E12 = expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E13 = expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E14 = expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E15 = expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK)
+    run:
+        shell("cat {input.E10} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E10}")
+        shell("cat {input.E11}| sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E11}")
+        shell("cat {input.E12} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E12}")
+        shell("cat {input.E13} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E13}")
+        shell("cat {input.E14} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E14}")
+        shell("cat {input.E15} | sort -k1,1 -k2,2n - | bedtools merge -i - > {output.E15}")
 
-# rule overlap_peaks:
-#     input:
-#         E10= expand(["results/macs2/{case}_vs_{control}_E10.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E11= expand(["results/macs2/{case}_vs_{control}_E11.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E12= expand(["results/macs2/{case}_vs_{control}_E12.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E13= expand(["results/macs2/{case}_vs_{control}_E13.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E14= expand(["results/macs2/{case}_vs_{control}_E14.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E15= expand(["results/macs2/{case}_vs_{control}_E15.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
-#         E10_pooled=expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#         E11_pooled=expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#         E12_pooled=expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#         E13_pooled=expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#         E14_pooled=expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#         E15_pooled=expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
-#     output:
-#         E10= expand("results/macs2/{mark}_E10.5_overlap.narrowPeak", mark=MARK),
-#         E11= expand("results/macs2/{mark}_E11.5_overlap.narrowPeak", mark=MARK),
-#         E12= expand("results/macs2/{mark}_E12.5_overlap.narrowPeak", mark=MARK),
-#         E13= expand("results/macs2/{mark}_E13.5_overlap.narrowPeak", mark=MARK),
-#         E14= expand("results/macs2/{mark}_E14.5_overlap.narrowPeak", mark=MARK),
-#         E15= expand("results/macs2/{mark}_E15.5_overlap.narrowPeak", mark=MARK)
-#     run:
-#         shell("python2.7 scripts/overlap_peaks.py {input.E10} {input.E10_pooled} {output.E10}")
-#         shell("python2.7 scripts/overlap_peaks.py {input.E11} {input.E11_pooled} {output.E11}")
-#         shell("python2.7 scripts/overlap_peaks.py {input.E12} {input.E12_pooled} {output.E12}")
-#         shell("python2.7 scripts/overlap_peaks.py {input.E13} {input.E13_pooled} {output.E13}")
-#         shell("python2.7 scripts/overlap_peaks.py {input.E14} {input.E14_pooled} {output.E14}")
-#         shell("python2.7 scripts/overlap_peaks.py {input.E15} {input.E15_pooled} {output.E15}")
+rule overlap_peaks:
+    input:
+        E10= expand(["results/macs2/{case}_vs_{control}_E10.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E11= expand(["results/macs2/{case}_vs_{control}_E11.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E12= expand(["results/macs2/{case}_vs_{control}_E12.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E13= expand(["results/macs2/{case}_vs_{control}_E13.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E14= expand(["results/macs2/{case}_vs_{control}_E14.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E15= expand(["results/macs2/{case}_vs_{control}_E15.5_{mark}_macs2_peaks.narrowPeak"], zip, case=IPS, control=INPUTS, mark=MARK),
+        E10_pooled=expand("results/macs2/E10.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E11_pooled=expand("results/macs2/E11.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E12_pooled=expand("results/macs2/E12.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E13_pooled=expand("results/macs2/E13.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E14_pooled=expand("results/macs2/E14.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+        E15_pooled=expand("results/macs2/E15.5_{mark}_macs2_pooled_peaks.narrowPeak", mark=MARK),
+    output:
+        E10= expand("results/macs2/{mark}_E10.5_overlap.narrowPeak", mark=MARK),
+        E11= expand("results/macs2/{mark}_E11.5_overlap.narrowPeak", mark=MARK),
+        E12= expand("results/macs2/{mark}_E12.5_overlap.narrowPeak", mark=MARK),
+        E13= expand("results/macs2/{mark}_E13.5_overlap.narrowPeak", mark=MARK),
+        E14= expand("results/macs2/{mark}_E14.5_overlap.narrowPeak", mark=MARK),
+        E15= expand("results/macs2/{mark}_E15.5_overlap.narrowPeak", mark=MARK)
+    run:
+        shell("python2.7 scripts/overlap_peaks.py {input.E10} {input.E10_pooled} {output.E10}")
+        shell("python2.7 scripts/overlap_peaks.py {input.E11} {input.E11_pooled} {output.E11}")
+        shell("python2.7 scripts/overlap_peaks.py {input.E12} {input.E12_pooled} {output.E12}")
+        shell("python2.7 scripts/overlap_peaks.py {input.E13} {input.E13_pooled} {output.E13}")
+        shell("python2.7 scripts/overlap_peaks.py {input.E14} {input.E14_pooled} {output.E14}")
+        shell("python2.7 scripts/overlap_peaks.py {input.E15} {input.E15_pooled} {output.E15}")
 
 # ===============================================================================================
 #  10. Combine all QC into multiqc output