call peaks on merged BAM files

dunnart/Snakefile

@@ -525,6 +525,37 @@ rule call_peaks_macs2:
         -n {params.name} \
         -g 2740338543 2> {log} "
 
+rule call_peaks_macs2_pooled_replicates:
+    input:
+        H3K4me3 = "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam",
+        H3K27ac = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam",
+        control27ac = "results/bowtie2/B-1_input_PPq30.sorted.dedup.bam",
+        control4me3 = "results/bowtie2/A-1_input_PPq30.sorted.dedup.bam"
+    output:
+        "results/macs2/H3K4me3_pooled_macs2_peaks.xls",
+        "results/macs2/H3K4me3_pooled_macs2_summits.bed",
+        "results/macs2/H3K4me3_pooled_macs2_peaks.narrowPeak",
+        "results/macs2/H3K27ac_pooled_macs2_peaks.xls",
+        "results/macs2/H3K27ac_pooled_macs2_summits.bed",
+        "results/macs2/H3K27ac_pooled_macs2_peaks.narrowPeak"
+    log:
+        H3K4me3 ="logs/H3K4me3_pooled_call_peaks_macs2.log",
+        H3K27ac ="logs/H3K27ac_pooled_call_peaks_macs2.log"
+    params:
+        H3K4me3 = "H3K4me3_pooled_macs2",
+        H3K27ac = "H3K27ac_pooled_macs2"
+    run:
+        shell(" macs2 callpeak -f BAMPE -t {input.H3K4me3} \
+        -c {input.control4me3} --keep-dup all \
+        --outdir results/macs2/ -p 0.01 \
+        -n {params.H3K4me3} \
+        -g 2740338543 2> {log.H3K4me3} ")
+        shell("macs2 callpeak -f BAMPE -t {input.H3K27ac} \
+        -c {input.control27ac} --keep-dup all \
+        --outdir results/macs2/ -p 0.01 \
+        -n {params.H3K27ac} \
+        -g 2740338543 2> {H3K27ac} ")
+
 # ===============================================================================================
 #  8. Peak QC
 #   > narrow peak counts