PeakFile to Homer Position File

for i in `ls 2.peak/*/*summit*`;do n=${i##*\/};n=${n%%_s*};awk '{print $4"\t"$1"\t"$2"\t"$3"\t+"}' ${i} >5.Motif/0.homerBed/${n}_homer.bed;done

1. Find Motif

findMotifsGenome.pl 5.Motif/0.homerBed/O1_H3K4me3_homer.bed hg38 5.Motif/1.Motif/O1_H3K4me3 -homer2 -p 50 -mask -bits -cache 5120 -size -250,250

结果文件

image.png

2. Peak Annotation

for i in `ls 5.Motif/0.homerBed/*homer.bed`;do n=${i##*\/};n=${n%%_h*};echo "annotatePeaks.pl ${i} hg38 > 5.Motif/2.peakAnnotation/${n}_peaks.annotation.bed";done  >5.Motif/2.peakAnnotation/0.run.sh

ps : Annotation

image.png

Although HOMER doesn't allow you to explicitly change the definition of the region that is the TSS (-1kb to +100bp), you can "do it yourself" by sorting the annotation output in EXCEL by the "Distance to nearest TSS" column, and selecting those within the range you are interested in.

结果文件

image.png