转录因子Chip-seq数据分析

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软件与流程

• 原始测序文件质控
  • FastQC
• 去除测序adapter序列
  • cutadapt
• chip-seq回帖
  • bowtie2、bwa mem
• bam文件排序建立索引
  · + samtools
• bam文件去重
  • picard
• Call peak
  • MACS2
• Peak区域的注释
  • Homer
• Peak区域motif的发现
  • MEME、DREME、STREME

测试数据

• ENCSR617IFZ

SAMPLES = [
    "CTCF-untreat",
    "CTCF-auxin2days"
]

REP_INFO = [
    "rep1",
    "rep2"
]


rule all:
    input:
        expand("macs2_result/mESC-ChIPSeq-{case_name}_{rep}_peaks.narrowPeak", case_name=SAMPLES, rep=REP_INFO)
    

rule call_peak:
    input:
        Input = "bam.bt2/mESC-ChIPSeq-Input_{rep}_bt2_hg38_sort_rmdup_MAPQ20.bam",
        PD = "bam.bt2/mESC-ChIPSeq-{case_name}_{rep}_bt2_hg38_sort_rmdup_MAPQ20.bam"
    output:
        "macs2_result/mESC-ChIPSeq-{case_name}_{rep}_peaks.narrowPeak"
    params:
        "mESC-ChIPSeq-{case_name}_{rep}",
        "macs2_result"
    log:
        "macs2_result/mESC-ChIPSeq-{case_name}_{rep}_macs2_callpeak.log"
    shell:
        "macs2 callpeak -c {input.Input} -t {input.PD} -f BAM -g mm --outdir {params[1]} -n {params[0]} --call-summits -m 5 50 -q 0.005 > {log}  2>&1 "

ChIPseeker: an R package for ChIP peak Annotation, Comparison and Visualization