From 4d8f22bd29e417d9336ce661f1b65efffe5242fb Mon Sep 17 00:00:00 2001
From: mpmeers <mpmeers@gmail.com>
Date: Fri, 9 Aug 2019 17:30:20 -0700
Subject: [PATCH] Update README.md

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 9412a37..8a8fea0 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ Here is some example code for converting from a paired-end BAM to a fragment bed
 	bedtools bamtobed -bedpe -i $sample.bam > $sample.bed
 	awk '$1==$4 && $6-$2 < 1000 {print $0}' $sample.bed > $sample.clean.bed
 	cut -f 1,2,6 $sample.clean.bed > $sample.fragments.bed
-	bedtools genomecov -i $sample.fragments.bed -g my.genome > $sample.fragments.bedgraph
+	bedtools genomecov -bg -i $sample.fragments.bed -g my.genome > $sample.fragments.bedgraph
 
 ## Output file: