{"id":678,"date":"2021-02-20T19:18:20","date_gmt":"2021-02-20T11:18:20","guid":{"rendered":"http:\/\/www.wuchangsong.com\/?p=678"},"modified":"2021-02-25T23:33:31","modified_gmt":"2021-02-25T15:33:31","slug":"mummer%e4%bd%bf%e7%94%a8%e5%8f%8a%e5%90%8e%e7%bb%ad%e7%bb%98%e5%9b%be","status":"publish","type":"post","link":"http:\/\/www.wuchangsong.com\/?p=678","title":{"rendered":"MUMmer\u4f7f\u7528\u53ca\u540e\u7eed\u7ed8\u56fe"},"content":{"rendered":"

MUMmer\u88ab\u5e7f\u6cdb\u7528\u4e8e\u5927\u7247\u6bb5\u5e8f\u5217\u7684\u6bd4\u5bf9\uff0c\u5982\u67d3\u8272\u4f53\u5171\u7ebf\u6027\u5206\u6790\u3002<\/p>\n

nucmer [options]  \r\ndelta-filter -i 80 -l 1000 -r -q out.delta > out.rq.delta\r\n#\u6bd4\u5bf9\u7387\u5927\u4e8e80%\uff0c\u5bf9\u6bd4\u957f\u5ea6\u5927\u4e8e1000\r\n#-r: \u4ec5\u4fdd\u7559\u6bcf\u4e2areference\u5728query\u4e0a\u7684\u6700\u4f73\u4f4d\u7f6e,\u5141\u8bb8\u591a\u6761reference\u5728query\u4e0a\u91cd\u53e0\r\n#-q: \u4ec5\u4fdd\u7559\u6bcf\u4e2aquery\u5728reference\u4e0a\u7684\u6700\u4f73\u4f4d\u7f6e,\u5141\u8bb8\u591a\u6761query\u5728reference\u4e0a\u91cd\u53e0\r\nshow-coords out.rq.delta > out.coords\r\ngrep -P  \"zfCh04\\s+\" out.coords|awk '{print $12,$13}' |sort |uniq -c #\u67e5\u770breference\u5355\u4e2a\u67d3\u8272\u4f53zfCh04\u548cquery\u4e0d\u540c\u67d3\u8272\u4f53\u7684\u5339\u914d\u533a\u57df\u7684\u6570\u91cf\r\ngrep -P  \"zfCh04\\s+gcCh04\" out.coords|awk '{print $12,$1,$2,$13,$4,$5}' > zfCh04_gcCh04.txt\r\nsed -i 's\/ \/\\t\/g' zfCh04_gcCh04.txt\r\n<\/pre>\n
#R\u4f5c\u56fe
\n\u4f7f\u7528RIdeogram\u5305\uff0c\u53ef\u53c2\u8003RIdeogram\uff1a\u67d3\u8272\u4f53\u6570\u636e\u53ef\u89c6\u5316\u7684R\u5305<\/a><\/p>\n
install.packages('RIdeogram')\r\nrequire(RIdeogram)\r\ncc <- read.table(\"111.xls\",sep=\"\\t\",header = TRUE,stringsAsFactors = F)\r\ndd <- read.table(\"222.xls\",sep=\"\\t\",header = TRUE,stringsAsFactors = F)\r\nideogram(karyotype = dd, synteny = cc)\r\n#data(karyotype_dual_comparison, package=\"RIdeogram\")\r\n#data(synteny_dual_comparison, package=\"RIdeogram\")\r\nideogram(karyotype = karyotype_dual_comparison, synteny = synteny_dual_comparison)\r\nconvertSVG(\"chromosome.svg\", device = \"png\")<\/pre>\n
karyotype_dual_comparison\u6587\u4ef6\u683c\u5f0f
\nChr: \u67d3\u8272\u4f53\u53f7
\nStart: \u8d77\u59cb
\nEnd: \u7ec8\u6b62
\nfill: \u67d3\u8272\u4f53\u586b\u5145\u8272
\nspecies\uff1a\u7269\u79cd\u540d
\nsize: \u7269\u79cd\u540d\u5b57\u4f53\u5927\u5c0f
\ncolor: \u7269\u79cd\u540d\u5b57\u4f53\u989c\u8272<\/p>\n
synteny_dual_comparison\u6587\u4ef6\u683c\u5f0f
\nSpecies_1\uff1a\u7269\u79cd1\u67d3\u8272\u4f53\u53f7
\nStart_1\uff0cEnd_1\uff1a\u7269\u79cd1\u67d3\u8272\u4f53\u533a\u57df\u4f4d\u7f6e
\nSpecies_2\uff1a\u7269\u79cd2\u67d3\u8272\u4f53\u53f7
\nStart_2\uff0cEnd_2\uff1a\u7269\u79cd2\u67d3\u8272\u4f53\u533a\u57df\u4f4d\u7f6e<\/p>\n
\u6b64\u5916\u8fd8\u652f\u6301\u4e09\u4e2a\u57fa\u56e0\u7ec4\u7684\u5171\u7ebf\u6027<\/p>\n","protected":false},"excerpt":{"rendered":"
MUMmer\u88ab\u5e7f\u6cdb\u7528\u4e8e\u5927\u7247\u6bb5\u5e8f\u5217\u7684\u6bd4\u5bf9\uff0c\u5982\u67d3\u8272\u4f53\u5171\u7ebf\u6027\u5206\u6790\u3002 nucmer [options] delta-filter -i 80 -l 1000 -r -q out.delta > out.rq.delta #\u6bd4\u5bf9\u7387\u5927\u4e8e80%\uff0c\u5bf9\u6bd4\u957f\u5ea6\u5927\u4e8e1000 #-r: \u4ec5\u4fdd\u7559\u6bcf\u4e2areference\u5728query\u4e0a\u7684\u6700\u4f73\u4f4d\u7f6e,\u5141\u8bb8\u591a\u6761reference\u5728query\u4e0a\u91cd\u53e0 #-q: \u4ec5\u4fdd\u7559\u6bcf\u4e2aquery\u5728reference\u4e0a\u7684\u6700\u4f73\u4f4d\u7f6e,\u5141\u8bb8\u591a\u6761query\u5728reference\u4e0a\u91cd\u53e0 show-coords out.rq.delta > out.coords grep -P “zfCh04\\s+” out.coords|awk ‘{print $12,$13}’ |sort |uniq -c #\u67e5\u770breference\u5355\u4e2a\u67d3\u8272\u4f53zfCh04\u548cquery\u4e0d\u540c\u67d3\u8272\u4f53\u7684\u5339\u914d\u533a\u57df\u7684\u6570\u91cf grep -P “zfCh04\\s+gcCh04” out.coords|awk ‘{print $12,$1,$2,$13,$4,$5}’ > zfCh04_gcCh04.txt sed -i ‘s\/ \/\\t\/g’ zfCh04_gcCh04.txt #R\u4f5c\u56fe \u4f7f\u7528RIdeogram\u5305\uff0c\u53ef\u53c2\u8003RIdeogram\uff1a\u67d3\u8272\u4f53\u6570\u636e\u53ef\u89c6\u5316\u7684R\u5305 install.packages(‘RIdeogram’) require(RIdeogram) cc <- read.table(“111.xls”,sep=”\\t”,header = TRUE,stringsAsFactors = […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4,10],"tags":[],"_links":{"self":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/678"}],"collection":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=678"}],"version-history":[{"count":7,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/678\/revisions"}],"predecessor-version":[{"id":693,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=\/wp\/v2\/posts\/678\/revisions\/693"}],"wp:attachment":[{"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=678"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=678"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.wuchangsong.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=678"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}