diff --git a/dunnart/Snakefile b/dunnart/Snakefile index ddc4a105e65e9de54fc7c548f366cf6cfa4784e1..597c6ca3a23a68cd5cb4227c70eda83b680ff6b3 100644 --- a/dunnart/Snakefile +++ b/dunnart/Snakefile @@ -189,6 +189,20 @@ rule indexBam: shell: "samtools index -c {input} {output} 2> {log}" +rule mergeBAMreplicates: + input: + H3K4me3 = ["results/bowtie2/A-2_H3K4me3_PPq30.sorted.dedup.bam, results/bowtie2/B-2_H3K4me3_PPq30.sorted.dedup.bam"], + H3K27ac = ["results/bowtie2/A-3_H3K27ac_PPq30.sorted.dedup.bam, results/bowtie2/B-3_H3K27ac_PPq30.sorted.dedup.bam"] + output: + H3K4me3 = "results/bowtie2/H3K4me3_pooled_PPq30.sorted.dedup.bam", + H3K27ac = "results/bowtie2/H3K27ac_pooled_PPq30.sorted.dedup.bam" + log: + H3K4me3 = "logs/H3K4me3.mergeBAM", + H3K27ac = "logs/H3K27ac.mergeBAM" + run: + shell("samtools merge {output.H3K4me3} {input.H3K4me3} 2> {log.H3K4me3}") + shell("samtools merge {output.H3K27ac} {input.H3K427ac} 2> {log.H3K27ac}") + # =============================================================================================== # 4. GENERAL ALIGNMENT QC # > SAMtools flagstat statistics