bedtools intersect差异片段分析

使用bedtools intersect寻找两个peaks文件的交集
帮助文档https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

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bedtools intersect -a $BAM/BED/GFF/VCF都支持（1个）
                             -b $BAM/BED/GFF/VCF都支持（可以比多个）
                             -v  #差异片段Only report those entries in A that have no overlap inB （A特有的）
                             -f 0.50 #Minimum overlap required as a fraction of A. Default is 1E-9 (i.e. 1bp)
                             -sorted #B过大的时候降低内存

我的数据试试
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bedtools intersect -b H3K4me3_hCG_0h_summits.bed -a H3K4me3_hCG_4h_summits.bed -wa -wb > diffpeak_H3K4me3_common.bed
bedtools intersect -b H3K4me3_hCG_0h_summits.bed -a H3K4me3_hCG_4h_summits.bed -v > diffpeak_H3K4me3_4hunique.bed
bedtools intersect -a H3K4me3_hCG_0h_summits.bed -b H3K4me3_hCG_4h_summits.bed -v > diffpeak_H3K4me3_0hunique.bed

然后利用bedToBam试一下画图再转bw###注意bed文件格式 chr start end score * ****这一列可以手动加上

bedtools bedtobam -i diffpeak_H3K4me3_0hunique.bed -g /storage2/anlei/reference/genome/mm10_USUC/sorted.chromosize.bed > diffpeak_H3K4me3_0hunique.bam
samtools sort -O bam -@50 diffpeak_H3K4me3_0hunique.bam -o diffpeak_H3K4me3_0hunique.sort.bam
samtools sort -O bam -@50 diffpeak_H3K4me3_0hunique.bam -o diffpeak_H3K4me3_0hunique.sort.bam
samtools index diffpeak_H3K4me3_0hunique.sort.bam
bamCoverage --bam diffpeak_H3K4me3_0hunique.sort.bam -o diffpeak_H3K4me3_0hunique.bw --normalizeUsing CPM -p 5

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bedtools multicov 可以用来对sorted and indexed bam文件依据已有的bed files进行reads计数

bedtools multicov