diff --git a/h3k4me3_processing.sh b/h3k4me3_processing.sh index 1c2f6b01a1f3d1b1a1341ea4aec46d7b3dd9f8da..8d9ee3d7045d00da5c3f8a51232ac9490da96307 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