{"id":26839,"date":"2024-01-29T17:20:32","date_gmt":"2024-01-29T09:20:32","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26839"},"modified":"2024-01-29T17:20:33","modified_gmt":"2024-01-29T09:20:33","slug":"%e5%b0%8f%e6%9e%9c%e7%9a%84circos%e8%af%be%e5%a0%82","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=26839","title":{"rendered":"\u5c0f\u679c\u7684Circos\u8bfe\u5802"},"content":{"rendered":"

1 Circos\u7b80\u4ecb<\/p>\n

\u76f8\u4fe1\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u6837\u5728\u67e5\u9605\u6587\u732e\u65f6\u5f80\u5f80\u60ca\u53f9\u4e8e\u6587\u4e2d\u56fe\u7247\u7684\u7eda\u70c2\u591a\u5f69\u548c\u7b80\u660e\u627c\u8981\uff0c\u6b63\u6240\u8c13\u201c\u4e00\u56fe\u80dc\u5343\u8a00\u201d\uff0c\u4e00\u5f20\u7ed3\u679c\u56fe\u5f80\u5f80\u53ef\u4ee5\u8ba9\u8bfb\u8005\u66f4\u76f4\u89c2\u660e\u767d\u7684\u4e86\u89e3\u6587\u732e\u7684\u6210\u679c\uff0c\u4f46\u662f\u5f80\u5f80\u4f17\u591a\u7684\u56fe\u7247\u53c8\u8ba9\u8bfb\u8005\u76ee\u4e0d\u6687\u63a5\uff0c\u6709\u6ca1\u6709\u529e\u6cd5\u5c06\u591a\u4e2a\u56fe\u7247\u7ec4\u5408\u4e3a\u4e00\u5f20\u56fe\u5462\uff1fCircos\u8bf4\uff1a\u6211\u53ef\u4ee5\uff01<\/p>\n

<\/p>\n

Circos\u662f\u4e00\u4e2a\u975e\u5e38\u5f3a\u5927\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u53ef\u89c6\u5316\u8f6f\u4ef6\uff0c\u4e0d\u4ec5\u53ef\u4ee5\u5c06\u57fa\u56e0\u7ec4\u4fe1\u606f\u5c55\u793a\u5728\u4e00\u4e2a\u4e2a\u540c\u5fc3\u5706\u4e0a\uff0c\u8fd8\u80fd\u901a\u8fc7\u8fde\u63a5\u7ebf\u7684\u65b9\u5f0f\u5c55\u793a\u57fa\u56e0\u7ec4\u533a\u5757\u4e4b\u95f4\u7684\u5173\u7cfb\u3002Circos\u4e4b\u7236\u662f\u4e00\u4f4d\u52a0\u62ff\u5927\u7684\u751f\u7269\u4fe1\u606f\u5b66\u5bb6Martin Krzywinski\uff0c\u4ed6\u8fd8\u6709\u7b2c\u4e8c\u4e2a\u8eab\u4efd\uff0c\u6444\u5f71\u5e08\uff0c\u8fd9\u5c31\u4e0d\u96be\u7406\u89e3\u4e3a\u4ec0\u4e48Circos\u56fe\u80fd\u5728\u5c55\u793a\u6570\u636e\u7684\u540c\u65f6\u53c8\u9887\u5177\u7f8e\u611f\u4e86\u3002<\/p>\n

2 Circos\u5b89\u88c5<\/p>\n

\u56e0\u4e3aCircos\u7684\u5b89\u88c5\u548c\u8fd0\u884c\u9700\u8981\u76f8\u5f53\u591a\u7684\u4f9d\u8d56\u6a21\u5757\uff08Perl\uff09\uff0c\u5c0f\u679c\u8fd9\u91cc\u63a8\u8350\u5728Ubuntu\u73af\u5883\u4e0b\u4f7f\u7528conda\u547d\u4ee4\u5b89\u88c5Circos\uff0c\u8fd8\u6709\u4ec0\u4e48\u6bd4\u4e00\u952e\u5b89\u88c5\u66f4\u7701\u5fc3\u7684\u5462\uff1f<\/p>\n

conda search circos #\u4f7f\u7528conda\u641c\u7d22circos\u4fe1\u606f<\/p>\n

conda install circos #conda\u4f1a\u81ea\u52a8\u5b89\u88c5\u6700\u65b0\u7248\u672c\u7684Circos<\/p>\n

\u8fd9\u6837conda\u5c31\u4f1a\u81ea\u52a8\u5b89\u88c5\u597dCircos\u53ca\u5176\u9700\u8981\u7684\u4f9d\u8d56\u6a21\u5757\u3002\u4f46\u662f\u4e5f\u6709\u4e2a\u522b\u5c0f\u4f19\u4f34\u8ddf\u5c0f\u679c\u53cd\u5e94\uff0c\u8fd9\u6837\u4ecd\u7136\u4f1a\u51fa\u73b0\u4f9d\u8d56\u6a21\u5757\u7f3a\u5931\u7684\u73b0\u8c61\u3002\u51fa\u73b0\u8fd9\u79cd\u95ee\u9898\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u5728\u6267\u884c\u4e0a\u8ff0\u4e24\u884c\u547d\u4ee4\u524d\u52a0\u4e24\u6761\u547d\u4ee4\uff1a<\/p>\n

conda create -n Circos #\u4f7f\u7528conda\u521b\u5efa\u4e00\u4e2a\u540d\u4e3aCircos\u7684\u73af\u5883<\/p>\n

conda activate Circos #\u8fdb\u5165\u6211\u4eec\u521b\u5efa\u7684\u8fd9\u4e2aCircos\u73af\u5883<\/p>\n

\u6ce8\u610f\u770b\u8fd9\u65f6\u7684\u73af\u5883\u540d\u79f0\u5c31\u7531base\u53d8\u6210Circos\u4e86\u3002<\/p>\n

<\/p>\n

\u8fd9\u6837\u518d\u8fdb\u884c\u5b89\u88c5\u5c31\u4e0d\u4f1a\u51fa\u73b0\u4f9d\u8d56\u6a21\u5757\u7f3a\u5931\u7684\u95ee\u9898\u4e86\u3002<\/p>\n

Circos\u7684\u64cd\u4f5c\u547d\u4ee4\u5341\u5206\u7b80\u5355\uff1a<\/p>\n

circos -conf circos.conf<\/p>\n

circos.conf\u662fCircos\u8fd0\u884c\u6240\u9700\u7684\u914d\u7f6e\u6587\u4ef6\uff0c\u4e0b\u9762\u5c0f\u679c\u63d0\u4f9b\u4e00\u4e2a\u7b80\u5355\u7684\u914d\u7f6e\u6587\u4ef6\uff1a<\/p>\n

karyotype = data\/karyotype\/karyotype.human.txt<\/p>\n

<ideogram><\/p>\n

<spacing><\/p>\n

default = 0.005r<\/p>\n

<\/spacing><\/p>\n

radius = 0.90r<\/p>\n

thickness = 20p<\/p>\n

fill = yes<\/p>\n

stroke_color = dgrey<\/p>\n

stroke_thickness = 2p<\/p>\n

<\/ideogram><\/p>\n

<image><\/p>\n

# Included from Circos distribution.<\/p>\n

<<include etc\/image.conf>><\/p>\n

<\/image><\/p>\n

<<include etc\/colors_fonts_patterns.conf>><\/p>\n

<<include etc\/housekeeping.conf>><\/p>\n

\u5982\u679cCircos\u6b63\u5e38\u8fd0\u884c\u5e76\u51fa\u56fe\u7684\u8bdd\uff0c\u90a3\u606d\u559c\u4f60\uff0c\u5df2\u7ecf\u6210\u529f\u6536\u83b7\u4e86\u753b\u56fe\u795e\u5668\u2014Circos\uff01<\/p>\n

<\/p>\n

\u5de5\u6b32\u5584\u5176\u4e8b\u5fc5\u5148\u5229\u5176\u5668\u3002\u65e2\u7136\u6211\u4eec\u6210\u529f\u5b89\u88c5\u4e86Circos\uff0c\u90a3\u4e0b\u9762\u5c31\u548c\u5c0f\u679c\u4e00\u8d77 \u63ed\u5f00Circos\u4f5c\u56fe\u7684\u795e\u79d8\u9762\u7eb1\u5427<\/p>\n

3 Circos\u7684\u914d\u7f6e\u6587\u4ef6<\/p>\n

\u6709\u4e9b\u5c0f\u4f19\u4f34\u5df2\u7ecf\u53d1\u73b0\u5c0f\u679c\u4e0a\u9762\u7684Circos\u56fe\u4e0e\u5176\u4ed6\u6587\u732e\u4e2d\u7684\u56fe\u76f8\u5dee\u751a\u8fdc\uff0c\u8fd9\u662f\u56e0\u4e3aCircos\u4f5c\u56fe\uff0c\u96be\u7684\u4ece\u6765\u4e0d\u662f\u8fd0\u884c\uff0c\u800c\u662f\u8f93\u5165\u6587\u4ef6\u7684\u5904\u7406\u548c\u51c6\u5907\u914d\u7f6e\u6587\u4ef6\u3002\u4e0b\u9762\u5c0f\u679c\u5c31\u5e26\u9886\u5927\u5bb6\u4e86\u89e3\u4e00\u4e0bCircos\u4f5c\u56fe\u6240\u9700\u7684\u914d\u7f6e\u6587\u4ef6\u3002<\/p>\n

\u9996\u5148\uff0c\u6211\u4eec\u9700\u8981\u7ed9Circos\u51c6\u5907\u4e00\u4e2a\u67d3\u8272\u4f53\u6838\u578b\u7684\u914d\u7f6e\u6587\u4ef6\uff0c\u53ea\u6709\u5148\u753b\u51fa\u57fa\u56e0\u7ec4\u7684\u67d3\u8272\u4f53\uff0c\u624d\u80fd\u540e\u7eed\u5728\u67d3\u8272\u4f53\u4e0a\u63cf\u8ff0\u4f17\u591a\u7684\u57fa\u56e0\u7ec4\u6570\u636e\u3002\u67d3\u8272\u4f53\u6838\u578b\u7684\u914d\u7f6e\u6587\u4ef6\u5982\u4e0b\u56fe\u6240\u793a\uff0c\u5206\u4e3a7\u5217\u3002<\/p>\n

<\/p>\n

\u5404\u5217\u7684\u542b\u4e49\u662f\uff1a<\/p>\n

Chr\/band\uff1achr\uff0c\u8fd9\u4e00\u5217\u5b9a\u4e49\u8868\u660e\u8fd9\u662f\u4e00\u4e2a\u67d3\u8272\u4f53\uff1bband\u8868\u660e\u8fd9\u662f\u4e00\u4e2a\u6761\u5e26\u3002<\/p>\n

-\/DOMAIN\uff1a\u77ed\u7ebf\u5360\u4f4d\u7b26\uff0c\u8fd9\u4e2a\u5360\u4f4d\u7b26\u901a\u5e38\u7528\u6765\u5b9a\u4e49\u6240\u5c5e\u5173\u7cfb\uff0c\u5bf9\u4e8e\u67d3\u8272\u4f53\u6765\u8bf4\uff0c\u6ca1\u6709\u6240\u5c5e\uff1bDOMAIN\u8868\u660e\u6240\u5c5e\u7684\u533a\u6bb5\u6216\u8005\u67d3\u8272\u4f53<\/p>\n

\u67d3\u8272\u4f53\u7f16\u53f7ID\uff1a ID\u662f\u67d3\u8272\u4f53\u552f\u4e00\u4e14\u4e0d\u80fd\u91cd\u590d\u7684\u6807\u8bc6\u3002\u5982\u679c\u4e00\u4e2a\u67d3\u8272\u4f53\u7ec4\u578b\u6587\u4ef6\u91cc\u9762\u5305\u542b\u591a\u4e2a\u4e0d\u540c\u6765\u6e90\u7684\u67d3\u8272\u4f53\u7ec4\uff0c\u8bbe\u7f6eID\u6700\u597d\u7684\u529e\u6cd5\u5c31\u662f\u4f7f\u7528\u524d\u7f00\u3002<\/p>\n

\u56fe\u7247\u540d\u79f0\uff1aLabel\u662f\u5c06\u6765\u7528\u4e8e\u663e\u793a\u5728\u56fe\u4e0a\u7684\u6587\u672c\u3002Label\u4e3b\u8981\u662f\u5728\u56fe\u4e2d\u663e\u793a\u7684\u540d\u79f0\uff0c\u5c0f\u679c\u8fd9\u91cc\u5c31\u76f4\u63a5\u4f7f\u75281,2, \u2026\u8868\u793a\uff0c\u4f46\u662f\u5982\u679c\u6709\u591a\u4e2a\u7269\u79cd\u7684\u57fa\u56e0\u7ec4\uff0c\u6216\u8005\u6765\u81ea\u4e0d\u540c\u7684\u54c1\u7cfb\uff0c\u8fd8\u662f\u8981\u52a0\u4ee5\u533a\u5206\u3002<\/p>\n

\u8d77\u59cb\u3001\u7ed3\u675f\uff1aSTART\u548cEND\u503c\uff0c\u5b9a\u4e49\u4e86\u67d3\u8272\u4f53\u7684\u5927\u5c0f\u3002\u5bf9\u4e8e\u67d3\u8272\u4f53\u6838\u578b\u6587\u4ef6\uff0c\u9700\u8981\u6307\u660e\u7684\u662f\uff0c\u8fd9\u91cc\u7684START\u548cEND\u5e94\u8be5\u662f\u67d3\u8272\u4f53\u672c\u8eab\u7684\u5927\u5c0f\uff0c\u800c\u4e0d\u662f\u4f60\u60f3\u7ed8\u5236\u90e8\u5206\u7684\u8d77\u6b62\u4f4d\u7f6e\u3002\u6307\u5b9a\u7ed8\u5236\u90e8\u5206\u5c06\u7531\u5176\u5b83\u6587\u4ef6\u6765\u5b9a\u4e49\u3002<\/p>\n

\u989c\u8272 \uff1aCOLOR\uff0c\u662f\u4e8e\u5b9a\u4e49\u663e\u793a\u7684\u989c\u8272\u3002\u5bf9\u4e8e\u4eba\u7c7b\u57fa\u56e0\u7ec4\u800c\u8a00\uff0ccircos\u9884\u8bbe\u4e86\u4e0e\u67d3\u8272\u4f53\u76f8\u540c\u7684\u540d\u5b57\u505a\u4e3a\u989c\u8272\u540d\uff0c\u6bd4\u5982chr1,chr2, \u2026chrX,chrY.<\/p>\n

\u660e\u767d\u4e86\u8fd9\u4e9b\uff0c\u5927\u5bb6\u5c31\u53ef\u4ee5\u7528\u81ea\u5df1\u7684\u6570\u636e\u51c6\u5907\u67d3\u8272\u4f53\u6838\u578b\u6587\u4ef6\u4e86\uff0c\u662f\u4e0d\u662f\u5f88\u7b80\u5355\u5462\uff1f<\/p>\n

\u5982\u679c\u6709\u751f\u4fe1\u5206\u6790\u7684\u9700\u8981\u53ef\u4ee5\u770b\u770b\u6211\u4eec\u63a8\u51fa\u7684\u751f\u4fe1\u4e91\u5e73\u53f0\u54e6<\/p>\n

\u7f51\u5740\uff1a\u4e91\u751f\u4fe1 – \u5b66\u751f\u7269\u4fe1\u606f\u5b66 (biocloudservice.com)<\/p>\n

\u5982\u679c\u5c0f\u4f19\u4f34\u6709\u5176\u4ed6\u6570\u636e\u5206\u6790\u9700\u6c42\uff0c\u53ef\u4ee5\u5c1d\u8bd5\u4f7f\u7528\u672c\u516c\u53f8\u65b0\u5f00\u53d1\u7684\u751f\u4fe1\u5206\u6790\u5c0f\u5de5\u5177\u4e91\u5e73\u53f0\uff0c\u96f6\u4ee3\u7801\u5b8c\u6210\u5206\u6790\uff0c\u975e\u5e38\u65b9\u4fbf\u5965\uff0c\u4e91\u5e73\u53f0\u7f51\u5740\u4e3a\uff1a(http:\/\/www.biocloudservice.com\/home.html)\uff0c\u5176\u4e2d\u4e5f\u5305\u62ec\u4e86\u901a\u8def\u8868\u8fbe\u5206\u6790(http:\/\/www.biocloudservice.com\/313\/313.php)\uff0c\u5355\u7ec6\u80de\u7684\u57fa\u56e0\u5171\u8868\u8fbe\u5206\u6790(http:\/\/www.biocloudservice.com\/906\/906.php)\u7b49\u5404\u79cd\u5c0f\u5de5\u5177\u54e6~\uff0c\u6709\u5174\u8da3\u7684\u5c0f\u4f19\u4f34\u53ef\u4ee5\u767b\u5f55\u7f51\u7ad9\u8fdb\u884c\u4e86\u89e3\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"

1 Circos\u7b80\u4ecb \u76f8\u4fe1\u5927\u5bb6\u548c\u5c0f\u679c\u4e00\u6837\u5728\u67e5\u9605\u6587\u732e\u65f6\u5f80\u5f80\u60ca\u53f9\u4e8e\u6587\u4e2d\u56fe\u7247\u7684\u7eda\u70c2\u591a\u5f69\u548c\u7b80\u660e\u627c\u8981\uff0c\u6b63\u6240\u8c13\u201c\u4e00\u56fe\u80dc\u5343\u8a00 […]<\/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\/26839"}],"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=26839"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26839\/revisions"}],"predecessor-version":[{"id":26847,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/26839\/revisions\/26847"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26839"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26839"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26839"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}