homer分析RNAseq数据

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Homer这个软件比较强大，主要做ChIP-Seq分析，除此之外，还可以做RNAseq以及microarray的分析
原文：http://homer.ucsd.edu/homer/motif/rnaMotifs.html
Analyzing Co-regulated Gene Lists for RNA motifs
用法：findMotifs.pl downregulated.genes.txt human-mRNA MotifOutput/ -rna -len 8
输入文件：3 mandatory arguments: A gene ID input file, the name of the promoter set (which is tied to an organism), and an output directory for all of the output files.
解释：输入文件downregulated.genes.txt为下调的gene list ，human-mRNA为promoter set，MotifOutput为输出文件夹
例子：

for sample in `ls *txt |cut -d '.' -f1`;do findMotifs.pl ${sample}.txt human ${sample}/ -start -400 -end 100 -len 8,10 -p 16 ;done

结果：

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相应的promoter或者genome安装：
查看可以安装的文件：perl /path-to-homer/configureHomer.pl -list
安装或者卸载： "-install <package name>" or "-remove <package name>".
如：
perl /path-to-homer/configureHomer.pl -install human
安装promoter则需要加“-p”,除此之外还有-o：organism -g genome
perl /path-to-homer/configureHomer.pl -install human-p

参考：http://homer.ucsd.edu/homer/microarray/index.html