From 0a431c063bed5e968578c8c4f847db177cc5f4e9 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <Venkat.Malladi@utsouthwestern.edu>
Date: Fri, 2 Dec 2016 14:09:03 -0600
Subject: [PATCH] Update h3k4me3 processing.

---
 h3k4me3_processing.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/h3k4me3_processing.sh b/h3k4me3_processing.sh
index 1c2f6b0..8d9ee3d 100644
--- a/h3k4me3_processing.sh
+++ b/h3k4me3_processing.sh
@@ -17,7 +17,7 @@ bedops --everything /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/
 
 # get peaks that are not represented in overlap peaks
 for i in $(ls /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/ES_D*narrowPeak); do bedtools intersect -v -wa -f 1.0 -r -a $i -b /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/overlap_peaks.narrowPeak​ >> /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/unique_peaks.narrowPeak; done
-    sort-bed /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/unique_peaks.narrowPeak | cut -f1,2,3 > /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/unique_peaks_sorted.narrowPeak
+sort-bed /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/unique_peaks.narrowPeak | cut -f1,2,3 > /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/unique_peaks_sorted.narrowPeak
 
 # Merge Peaks and Union of peaks
 bedops -m --range -1 /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/overlap_peaks.narrowPeak​ > /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k4me3/merge_overlap_peaks.bed
-- 
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