diff --git a/Step_2/Step2_Final_PeakCalls.sh.txt b/Step_2/Step2_Final_PeakCalls.sh.txt new file mode 100644 index 0000000000000000000000000000000000000000..bb70018d63da6f3da5caaca2fb399f09acddf7e4 --- /dev/null +++ b/Step_2/Step2_Final_PeakCalls.sh.txt @@ -0,0 +1,26 @@ +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