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Commit 9d9a5490 authored by Laura Cook's avatar Laura Cook
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merge BAM files for replicates

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...@@ -189,6 +189,20 @@ rule indexBam: ...@@ -189,6 +189,20 @@ rule indexBam:
shell: shell:
"samtools index -c {input} {output} 2> {log}" "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 # 4. GENERAL ALIGNMENT QC
# > SAMtools flagstat statistics # > SAMtools flagstat statistics
......
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