ChIP-seq流程(MACS2 histone peaks)

ChIP-seq（流程）

1，质量控制

基于FastQC和Trimmomatic：

fastqc -t 5 input.fastq.gz
java -jar ~/tools/Trimmomatic/Trimmomatic-0.36/trimmomatic-0.36.jar SE -threads 12 -phred33 -trimlog BSY-trim.log ENCFF000BSY.fastq ENCFF000BSY-trim.fastq ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

根据FastQC报告，选择phred33或者phred64。

Remove adapters (ILLUMINACLIP:TruSeq3-SE:2:30:10)

Remove leading low quality or N bases (LEADING:3)

Remove trailing low quality or N bases (TRAILING:3)

Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (SLIDINGWINDOW:4:15)

Drop reads below the 36 bases long (MINLEN:36)