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Step_2/Step2_Final_PeakCalls.sh.txt

+module load MACS2
+
+macs2 callpeak \
+        --treatment /data/user/rphill3/Enhancer_Ident_ATAC/Str_ATAC_merged.bam \
+        --qvalue 0.00001 \
+        --gsize 2729862089 \
+        --format BAMPE \
+        --outdir /data/user/rphill3/Enhancer_Ident_ATAC/Final_PeakCalls \
+        --name Str_Merged_BAMPE_narrow_0.00001_FinalPeaks
+
+macs2 callpeak \
+        --treatment /data/user/rphill3/Enhancer_Ident_ATAC/Cor_ATAC_merged.bam \
+        --qvalue 0.00001 \
+        --gsize 2729862089 \
+        --format BAMPE \
+        --outdir /data/user/rphill3/Enhancer_Ident_ATAC/Final_PeakCalls \
+        --name Cor_Merged_BAMPE_narrow_0.00001_FinalPeaks
+
+
+macs2 callpeak \
+        --treatment /data/user/rphill3/Enhancer_Ident_ATAC/Hpc_ATAC_merged.bam \
+        --qvalue 0.00001 \
+        --gsize 2729862089 \
+        --format BAMPE \
+        --outdir /data/user/rphill3/Enhancer_Ident_ATAC/Final_PeakCalls \
+        --name Hpc_Merged_BAMPE_narrow_0.00001_FinalPeaks