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Commit d27b44fc authored by Venkat Malladi's avatar Venkat Malladi
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Update H3K27ac analysis.

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h3k27ac_processing.sh
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View file @ d27b44fc
......@@ -20,7 +20,7 @@ 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_h3k27ac/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_h3k27ac/overlap_peaks.narrowPeak​ >> /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k27ac/unique_peaks.narrowPeak; done
sort-bed /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k27ac/unique_peaks.narrowPeak | cut -f1,2,3 > /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k27ac/unique_peaks_sorted.narrowPeak
sort-bed /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k27ac/unique_peaks.narrowPeak | cut -f1,2,3 > /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k27ac/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_h3k27ac/overlap_peaks.narrowPeak​ > /project/GCRB/Lee_Lab/s163035/Matrix_analysis_PMIT_25842977/ChIP-seq/universe_h3k27ac/merge_overlap_peaks.bed
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universe_enhancer_H3K27ac.bed
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View file @ d27b44fc
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