{"id":48928,"date":"2024-06-15T20:08:25","date_gmt":"2024-06-15T12:08:25","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=48928"},"modified":"2024-06-15T23:32:36","modified_gmt":"2024-06-15T15:32:36","slug":"%e5%b0%8f%e6%9e%9c%e5%b8%a6%e4%bd%a0%e7%94%a8homer%e8%bf%9b%e8%a1%8cmotif%e5%af%8c%e9%9b%86%e5%88%86%e6%9e%90-3","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=48928","title":{"rendered":"\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790"},"content":{"rendered":"
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\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790<\/a><\/h1>\n
\u539f\u521b\u00a0\u00a0<\/span>\u5c0f\u679c\u00a0\u00a0<\/span><\/a>\u751f\u4fe1\u679c\u00a0\u00a0<\/span>2023-03-14 19:00:49<\/em><\/div>\n

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Homer\u662f\u5e72\u561b\u7684\uff1f<\/span><\/span><\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n
HOMER\u662f\u4e00\u5957\u57fa\u4e8e <\/span>C++ <\/span>\u548c <\/span>Perl <\/span>\u8bed\u8a00\u7684\u7528\u4e8e <\/span>motif <\/span>\u67e5\u627e\u548c\u4e8c\u4ee3\u6570\u636e\u5206\u6790\u7684\u5de5\u5177\uff0c\u4e00\u822c\u9700\u8981\u4e24\u4e2a\u5e8f\u5217\u4f5c\u4e3a\u53c2\u6570\uff1a<\/span><\/span><\/p>\n

\u25cf <\/span>\u53c2\u8003\u5e8f\u5217\uff1a<\/span>hg19<\/span>\u3001<\/span>mm10 <\/span>\u7b49\u57fa\u56e0\u7ec4\u5e8f\u5217\u3001<\/span>promoter <\/span>\u5e8f\u5217\u3001\u81ea\u5b9a\u4e49\u7684 <\/span>FASTA <\/span>\u5e8f\u5217<\/span><\/span><\/p>\n

\u25cf <\/span>\u6240\u8981\u5206\u6790\u7684\u5e8f\u5217\uff1a<\/span>DNA <\/span>\u6216 <\/span>RNA <\/span>\u5e8f\u5217<\/span><\/span><\/p>\n

HOMER \u9002\u7528\u4e8e\u5728\u5927\u89c4\u6a21\u6570\u636e\u4e2d\u5bfb\u627e <\/span>DNA <\/span>\u6216 <\/span>RNA <\/span>\u5e8f\u5217\u7684 <\/span>motif<\/span>\u3002<\/span><\/span><\/p>\n<\/section>\n

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\u00a0\u90a3\u4ec0\u4e48\u662f <\/span>motif <\/span>\u5462\uff1f<\/span><\/span><\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n
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motif\uff1a\u53cd\u590d\u51fa\u73b0\u7684\u6a21\u5f0f\uff0c\u5373\u4e00\u79cd\u7279\u5f81\u5e8f\u5217\uff0c\u6bd4\u5982 <\/span>sequence motif, structure motif, network motif<\/span>\u3002\u5b83\u6709\u6216\u8005\u53ef\u80fd\u6709\u4e00\u5b9a\u7684\u751f\u7269\u5b66\u529f\u80fd\u3002<\/span><\/span><\/p>\n<\/section>\n

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\u5177\u4f53\u5206\u6790\u6b65\u9aa4<\/span><\/strong><\/p>\n<\/section>\n<\/section>\n<\/section>\n

3.1 linux\u914d\u7f6e\u65b0\u73af\u5883<\/span><\/span><\/strong><\/span><\/p>\n

conda create -n work puthon=3.8<\/span><\/p>\n

conda activate work<\/span><\/p>\n

3.2 homer\u5b89\u88c5<\/span><\/span><\/strong><\/span><\/p>\n

conda install -c bioconda homer<\/span><\/p>\n

##\u4e0b\u8f7d<\/span>configureHomer.pl<\/span><\/span><\/p>\n

wget http:\/\/homer.ucsd.edu\/homer\/configureHomer.pl<\/span><\/p>\n

##\u4f7f\u7528<\/span>configureHomer.pl<\/span>\u914d\u7f6e<\/span>Homer<\/span><\/span><\/p>\n

perl configureHomer.pl -install \u00a0<\/span><\/p>\n

perl configureHomer.pl -install mm10<\/span><\/p>\n

3.3 homer\u5206\u6790<\/span><\/span><\/strong><\/span><\/p>\n

3.3.1 Analyzing lists of genes with promoter motif analysis (findMotifs.pl)<\/span><\/strong><\/span><\/p>\n

############\u5bfb\u627e\u57fa\u56e0\u5217\u8868\u542f\u52a8\u5b50\u4e0a\u7684<\/span>motif<\/span>\u5bcc\u96c6<\/span><\/span><\/p>\n

findMotifs.pl 3v3135F15Q001gene.txt mouse \/public\/home\/wjiang\/zhan\/work\/homer\/testdata -len 10<\/span><\/p>\n

3.3.2 Analyzing genomic positions(findMotifsGenome.pl)<\/span><\/strong><\/span><\/p>\n

####\u8f93\u5165\u4e3a<\/span>bed<\/span>\u6587\u4ef6\uff0c\u4e3b\u8981\u662f<\/span>chip-seq<\/span>\u6570\u636e\u901a\u8fc7<\/span>macs2 callpeak<\/span>\u4ea7\u751f<\/span>narrowPeak<\/span>\u6587\u4ef6\uff0c\u9700\u8981\u9996\u5148\u5904\u7406\u4e00\u4e0b\u3002<\/span><\/span><\/p>\n

awk ‘{print $4″t”$1″t”$2″t”$3″t+”}’ chirp_06ab_peaks.narrowPeak > chirp_06ab_homer.bed<\/span><\/p>\n

for i in *_homer.bed;do j=${i%_homer.bed}; bsub -J macs2p -e %J.err -o %J.out -R span[hosts=1] -n 1 “findMotifsGenome.pl $i mm10 $j -len 8,10,12”;done<\/span><\/p>\n

3.3.3 Analyzing custom FASTA files (findMotifs.pl, homer2)<\/span><\/strong><\/span><\/p>\n

homers\u7684\u8bf4\u660e\u6587\u6863\uff1a<\/span>recommended that you have both target and background sequences, and in each case you should have several (preferably thousands) of sequences in each set that are roughly the same length<\/span>\u3002<\/span><\/span><\/p>\n

\u9700\u8981\u76ee\u7684\u548c\u80cc\u666f\u57fa\u56e0\u7684\u5e8f\u5217\uff0c\u6240\u4ee5\u8fd9\u4e2a\u4e00\u822c\u7528\u7684\u6bd4\u8f83\u5c11\u4e00\u4e9b\u3002<\/span><\/span><\/p>\n

3.3.4 Analyzing data for RNA motifs (findMotifs.pl\/findMotifsGenome.pl)<\/span><\/strong><\/span><\/p>\n

####\u548c\u5bfb\u627e<\/span>DNA<\/span>\u5e8f\u5217\u7684<\/span>motif<\/span>\u533a\u522b\u5728\u4e8e\uff1a\u4f7f\u7528 <\/span>findMotifs.pl<\/span>\u548c <\/span>findMotifsGenome.pl<\/span>\u65f6\uff0c\u8981\u52a0\u4e0a <\/span>\u201c-rna\u201d<\/span>\u53c2\u6570\uff0c\u4ece\u800c\u53ea\u5bfb\u627e<\/span>RNA+<\/span>\u94fe\u7684<\/span>motif<\/span>\uff0c\u5e76\u4e14\u5339\u914d<\/span>\/<\/span>\u663e\u793a<\/span>U<\/span>\u800c\u4e0d\u662f<\/span>T<\/span>\u3002<\/span><\/span><\/p>\n

#######\u6ce8\u610f\uff01<\/span>HOMER<\/span>\u5c1a\u672a\u5305\u542b<\/span>\u201cRNA motif\u201d<\/span>\u5217\u8868\uff0c\u6240\u4ee5\u4e0d\u652f\u6301<\/span>\u201c<\/span>\u5df2\u77e5<\/span>motif\u201d<\/span>\u7684\u5206\u6790\u3002\u5982\u679c\u4f7f\u7528<\/span>FASTA<\/span>\u6587\u4ef6\u683c\u5f0f\uff0c\u8bf7\u5728\u8f93\u5165\u6587\u4ef6\u4e2d\u4f7f\u7528<\/span>T<\/span>\uff08<\/span>DNA<\/span>\u7f16\u7801\uff09\u3002<\/span><\/span><\/p>\n

# \u83b7\u53d6\u76ee\u6807\u5e8f\u5217\u5728\u4eba\u7c7b<\/span>mRNA<\/span>\u4e0a\u805a\u96c6\u7684<\/span>motif<\/span><\/span><\/p>\n

findMotifs.pl genes.txt mouse MotifOutput\/ -rna -len 8<\/span><\/p>\n

# \u5206\u6790<\/span>CLIP-Seq for RNA motifs<\/span><\/span><\/p>\n

findMotifsGenome.pl fox2.clip.bed hg17 MotifOutput -rna<\/span><\/p>\n

3.3.5 Scanning for motif across the entire genome (scanMotifGenomeWide.pl)<\/span><\/strong><\/span><\/p>\n

scanMotifGenomeWide.pl pu1.motif mm9 -bed > pu1.sites.mm9.bed<\/span><\/p>\n

########\u8fd9\u4e2a\u7684\u8bdd\uff0c<\/span><\/span>\u5176\u5b9e<\/span>\u7528<\/span>MEME\u6570\u636e\u5e93\u4e2d\u7684<\/span>FIMO<\/span>\u6548\u679c\u66f4\u597d\u4e00\u4e9b<\/span><\/span><\/p>\n

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\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/p>\n

\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/p>\n

\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/p>\n

\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n

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\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790 \u539f\u521b\u00a0\u00a0\u5c0f\u679c\u00a0\u00a0\u751f\u4fe1\u679c\u00a0\u00a02023-03-14 19:00:49 […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48928"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=48928"}],"version-history":[{"count":2,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48928\/revisions"}],"predecessor-version":[{"id":49015,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/48928\/revisions\/49015"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=48928"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=48928"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=48928"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}