{"id":29026,"date":"2024-02-20T17:38:10","date_gmt":"2024-02-20T09:38:10","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29026"},"modified":"2024-02-20T17:38:12","modified_gmt":"2024-02-20T09:38:12","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","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=29026","title":{"rendered":"\u5c0f\u679c\u5e26\u4f60\u7528homer\u8fdb\u884cmotif\u5bcc\u96c6\u5206\u6790"},"content":{"rendered":"<p><strong>1 Homer\u662f\u5e72\u561b\u7684\uff1f<\/strong><\/p>\n<p>HOMER\u662f\u4e00\u5957\u57fa\u4e8e C++ \u548c Perl \u8bed\u8a00\u7684\u7528\u4e8e motif \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<\/p>\n<p>\u25cf \u53c2\u8003\u5e8f\u5217\uff1ahg19\u3001mm10 \u7b49\u57fa\u56e0\u7ec4\u5e8f\u5217\u3001promoter \u5e8f\u5217\u3001\u81ea\u5b9a\u4e49\u7684 FASTA \u5e8f\u5217<\/p>\n<p>\u25cf \u6240\u8981\u5206\u6790\u7684\u5e8f\u5217\uff1aDNA \u6216 RNA \u5e8f\u5217<\/p>\n<p>HOMER \u9002\u7528\u4e8e\u5728\u5927\u89c4\u6a21\u6570\u636e\u4e2d\u5bfb\u627e DNA \u6216 RNA \u5e8f\u5217\u7684 motif\u3002<\/p>\n<p><strong>2 \u90a3\u4ec0\u4e48\u662f motif \u5462\uff1f<\/strong><\/p>\n<p>motif\uff1a\u53cd\u590d\u51fa\u73b0\u7684\u6a21\u5f0f\uff0c\u5373\u4e00\u79cd\u7279\u5f81\u5e8f\u5217\uff0c\u6bd4\u5982 sequence motif, structure motif, network motif\u3002\u5b83\u6709\u6216\u8005\u53ef\u80fd\u6709\u4e00\u5b9a\u7684\u751f\u7269\u5b66\u529f\u80fd\u3002<\/p>\n<p><strong>3 \u5177\u4f53\u5206\u6790\u6b65\u9aa4<\/strong><\/p>\n<p><strong>3.1 linux\u914d\u7f6e\u65b0\u73af\u5883<\/strong><\/p>\n<p>conda create -n work puthon=3.8<\/p>\n<p>conda activate work<\/p>\n<p><strong>3.2 homer\u5b89\u88c5<\/strong><\/p>\n<p>conda install -c bioconda homer<\/p>\n<p>##\u4e0b\u8f7dconfigureHomer.pl<\/p>\n<p>wget http:\/\/homer.ucsd.edu\/homer\/configureHomer.pl<\/p>\n<p>##\u4f7f\u7528configureHomer.pl\u914d\u7f6eHomer<\/p>\n<p>perl configureHomer.pl -install<\/p>\n<p>perl configureHomer.pl -install mm10<\/p>\n<p><strong>3.3 homer\u5206\u6790<\/strong><\/p>\n<p><strong>3.3.1 Analyzing lists of genes with promoter motif analysis (findMotifs.pl)<\/strong><\/p>\n<p>############\u5bfb\u627e\u57fa\u56e0\u5217\u8868\u542f\u52a8\u5b50\u4e0a\u7684motif\u5bcc\u96c6<\/p>\n<p>findMotifs.pl 3v3135F15Q001gene.txt mouse \/public\/home\/wjiang\/zhan\/work\/homer\/testdata -len 10<\/p>\n<p><strong>3.3.2 Analyzing genomic positions(findMotifsGenome.pl)<\/strong><\/p>\n<p>####\u8f93\u5165\u4e3abed\u6587\u4ef6\uff0c\u4e3b\u8981\u662fchip-seq\u6570\u636e\u901a\u8fc7macs2 callpeak\u4ea7\u751fnarrowPeak\u6587\u4ef6\uff0c\u9700\u8981\u9996\u5148\u5904\u7406\u4e00\u4e0b\u3002<\/p>\n<p>awk &#8216;{print $4&#8243;\\t&#8221;$1&#8243;\\t&#8221;$2&#8243;\\t&#8221;$3&#8243;\\t+&#8221;}&#8217; chirp_06ab_peaks.narrowPeak &gt; chirp_06ab_homer.bed<\/p>\n<p>for i in *_homer.bed;do j=${i%_homer.bed}; bsub -J macs2p -e %J.err -o %J.out -R span[hosts=1] -n 1 &#8220;findMotifsGenome.pl $i mm10 $j -len 8,10,12&#8221;;done<\/p>\n<p><strong>3.3.3 Analyzing custom FASTA files (findMotifs.pl, homer2)<\/strong><\/p>\n<p>homers\u7684\u8bf4\u660e\u6587\u6863\uff1arecommended 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\u3002<\/p>\n<p>\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<\/p>\n<p><strong>3.3.4 Analyzing data for RNA motifs (findMotifs.pl\/findMotifsGenome.pl)<\/strong><\/p>\n<p>####\u548c\u5bfb\u627eDNA\u5e8f\u5217\u7684motif\u533a\u522b\u5728\u4e8e\uff1a\u4f7f\u7528 findMotifs.pl\u548c findMotifsGenome.pl\u65f6\uff0c\u8981\u52a0\u4e0a \u201c-rna\u201d\u53c2\u6570\uff0c\u4ece\u800c\u53ea\u5bfb\u627eRNA+\u94fe\u7684motif\uff0c\u5e76\u4e14\u5339\u914d\/\u663e\u793aU\u800c\u4e0d\u662fT\u3002<\/p>\n<p>#######\u6ce8\u610f\uff01HOMER\u5c1a\u672a\u5305\u542b\u201cRNA motif\u201d\u5217\u8868\uff0c\u6240\u4ee5\u4e0d\u652f\u6301\u201c\u5df2\u77e5motif\u201d\u7684\u5206\u6790\u3002\u5982\u679c\u4f7f\u7528FASTA\u6587\u4ef6\u683c\u5f0f\uff0c\u8bf7\u5728\u8f93\u5165\u6587\u4ef6\u4e2d\u4f7f\u7528T\uff08DNA\u7f16\u7801\uff09\u3002<\/p>\n<p># \u83b7\u53d6\u76ee\u6807\u5e8f\u5217\u5728\u4eba\u7c7bmRNA\u4e0a\u805a\u96c6\u7684motif<\/p>\n<p>findMotifs.pl genes.txt mouse MotifOutput\/ -rna -len 8<\/p>\n<p># \u5206\u6790CLIP-Seq for RNA motifs<\/p>\n<p>findMotifsGenome.pl fox2.clip.bed hg17 MotifOutput -rna<\/p>\n<p><strong>3.3.5 Scanning for motif across the entire genome (scanMotifGenomeWide.pl)<\/strong><\/p>\n<p>scanMotifGenomeWide.pl pu1.motif mm9 -bed &gt; pu1.sites.mm9.bed<\/p>\n<p>########\u8fd9\u4e2a\u7684\u8bdd\uff0c\u5176\u5b9e\u7528MEME\u6570\u636e\u5e93\u4e2d\u7684FIMO\u6548\u679c\u66f4\u597d\u4e00\u4e9b<\/p>\n","protected":false},"excerpt":{"rendered":"<p>1 Homer\u662f\u5e72\u561b\u7684\uff1f HOMER\u662f\u4e00\u5957\u57fa\u4e8e C++ \u548c Perl \u8bed\u8a00\u7684\u7528\u4e8e motif \u67e5\u627e\u548c\u4e8c\u4ee3\u6570\u636e\u5206 [&hellip;]<\/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\/29026"}],"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=29026"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29026\/revisions"}],"predecessor-version":[{"id":29029,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/29026\/revisions\/29029"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29026"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29026"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29026"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}