motif富集分析

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HOMER 工具

1. scanMotifGenomeWide.pl

给定motif序列，在指定基因组上检索，并且注释所在位置。

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cd ~/anaconda3/envs/py36/share/homer/bin
scanMotifGenomeWide.pl /media/ggj/NEW/DifferentiationForce/xbp1/xbp1-Genome/custom_xbp1.motif   hg38 -bed > xbp1.sites.hg388.bed

awk '{print $4"\t"$1"\t"$2"\t"$3"\t"$6}' /media/ggj/NEW/DifferentiationForce/xbp1/xbp1-Genome/wholeGenome/xbp1.sites.hg388.bed > homer_peaks.tmp

annotatePeaks.pl homer_peaks.tmp hg38 1> xbp1.sites.hg388.peaksAnno.xls 2> xbp1.sites.hg388.annLog.txt
2. findMotifsGenome.pl / findMotifs.pl

There are 3 basic ways to run HOMER - with FASTA files, with Gene Identifiers, or from Genomic Positions.

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## 生成背景文件
scrambleFasta.pl Erythroid_seq.fa >background.fa
## 输入fasta文件，只能包含一条序列
homer2 denovo -i Erythroid_seq_sample.fa -b background.fa  > ./homer/example.txt
格式转换

http://embnet.ccg.unam.mx/rsat/convert-matrix_form.cgi

MEME to PFM