想寫這個純粹是 不想每次call peak 都全網(wǎng)找參數(shù)

1.Macs2 參數(shù)

1. Narrow Peak

macs2 callpeak -c ${n1}_input/*/*last*bam -t ${i} -g hs -q 0.01 --nomodel --call-summits -f BAMPE --outdir 1.Macs2.peak/${n} -n ${n} -q 0.01 2>1.Macs2.peak/logs/${n}.log

2. Broad Peak

macs2 callpeak -c 0.Bam/1.last.bam/Vector_input.bam -t 0.Bam/1.last.bam/Vector_H3K9me3_3.bam -g hs --nomodel --broad --broad-cutoff 0.1 -f BAMPE --outdir 1.peak/Vector_H3K9me3_3 -n Vector_H3K9me3_3 -B --SPMR 2>1.peak/logs/Vector_H3K9me3_3.log

單端測序文件類似，注意Paired-End mode is off

2. 結(jié)果文件
   1）NarrowPeak
   BED6+4格式，包含peak位置信息，peak summit, pvalue and qvalue，可以使用UCSC genome browser查看。其中幾列信息如下：
   5th: integer score for display
   7th: fold-change
   8th: -log10pvalue
   9th: -log10qvalue
   10th: relative summit position to peak start

2）prefix_treat_pileup.bdg 文件為輸入文件treat組的bedGraph file，MACS will save fragment pileup signal per million reads

鏈接：https://www.imooc.com/article/270403