From aa21fb823a91e0f3762fb277340534a2edcec80e Mon Sep 17 00:00:00 2001
From: mpmeers <mpmeers@gmail.com>
Date: Fri, 9 Aug 2019 17:29:58 -0700
Subject: [PATCH] Update README.md

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 6cc4e79..9412a37 100644
--- a/README.md
+++ b/README.md
@@ -44,8 +44,8 @@ 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 > $fragments.bed
-	bedtools genomecov -i $fragments.bed -g my.genome > $fragments.bedgraph
+	cut -f 1,2,6 $sample.clean.bed > $sample.fragments.bed
+	bedtools genomecov -i $sample.fragments.bed -g my.genome > $sample.fragments.bedgraph
 
 ## Output file: