Update h3k4me3 processing.

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