Update ATACflow.md

Wednesday/ATACflow.md

@@ -100,7 +100,7 @@ fragment_size_distribution:
 
 bamCoverage:
     do: yes
-    options: "--outFileFormat bigwig --extendReads --binSize 1 --effectiveGenomeSize 2913022398 --normalizeUsing RPKM" 
+    options: "--outFileFormat bigwig --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC" 
     threads: 4
 
 
@@ -129,8 +129,8 @@ macs2_peakcalling:
     do : yes
     cutoff: 0.01
     genomeSize: mm
-    extsize : 100
-    options: ""
+    extsize : 200
+    options: "--shift -100 --keep-dup all"
 
 ```
 
@@ -169,4 +169,4 @@ adapters:
     options: -O 6  -u -50 -U 50
     quality: 30
     threads: 4
-```
\ No newline at end of file
+```