{"id":819,"date":"2013-04-08T10:58:46","date_gmt":"2013-04-08T02:58:46","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=819"},"modified":"2013-06-19T11:17:38","modified_gmt":"2013-06-19T03:17:38","slug":"quake%e7%9a%84%e5%ae%89%e8%a3%85%e5%92%8c%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=819","title":{"rendered":"Quake\u7684\u5b89\u88c5\u548c\u4f7f\u7528"},"content":{"rendered":"

\u4e00. Quake\u7b80\u4ecb<\/h1>\n

Quake<\/a>\u662f\u7531CBCB(Center for Bioinformatics and Computational Biology)<\/a>\u5f00\u53d1\u7684\u8fd0\u7528\u4e8e\u4fee\u6b63\u5e8f\u5217\u9519\u8bef\u7684\u8f6f\u4ef6\u3002Quake\u91c7\u7528k-mer\u7684\u9519\u8bef\u4fee\u6b63\u65b9\u5f0f\uff0c\u7279\u522b\u9002\u5408\u4e8eIllumina\u6d4b\u5e8f\u7684short reads\u6570\u636e,\u5c06reads\u4e2d\u7684\u9519\u8bef\u78b1\u57fa\u8fdb\u884c\u4fee\u6b63\uff0c\u540c\u65f6\uff0c\u5fc5\u987b\u8981\u6ee1\u8db3\u78b1\u57fa\u7684\u57fa\u56e0\u7ec4\u8986\u76d6\u5ea6\u8981>15X\u3002\u5176\u6587\u7ae0<\/a>2010\u5e74\u53d1\u8868\u5728Genome Biology<\/a>\u4e0a\u3002<\/p>\n

\u4e8c. Quake\u7684\u5b89\u88c5<\/h1>\n

1. \u4e0b\u8f7d\u5e76\u5b89\u88c5Boost<\/a>
\n2. \u4e0b\u8f7dQuake\u5e76\u5b89\u88c5<\/p>\n

$ wget http:\/\/www.cbcb.umd.edu\/software\/quake\/downloads\/quake-0.3.4.tar.gz\r\n$ tar zxf quake-0.3.4.tar.gz\r\n$ cd Quake\/src\r\n$ make<\/pre>\n
3. \u5b89\u88c5JELLYISH<\/a>\uff0c\u5e76\u5c06jellyfish\u94fe\u63a5\u5230quake<\/p>\n
$ ln -s ....\/jellyfish ..\/bin\/jellyfish\r\n\u8fd9\u4e00\u6b65\u9700\u8981\u5b89\u88c5jellyfish\uff0c\u7136\u540e\u5c06\u5176\u8f6f\u94fe\u63a5\u5230Quake\u7684bin\u76ee\u5f55\u4e0b\u3002\u6216\u8005\u4fee\u6539Quake\u7684bin\r\n\u76ee\u5f55\u4e0b\u7684quake.py\u811a\u672c\uff0c\u5c06jellyfish\u6240\u5728\u7684\u76ee\u5f55\u8fdb\u884c\u4fee\u6b63\u3002<\/pre>\n
4. \u5b89\u88c5R\u53caR\u7684\u8f6f\u4ef6\u5305VGAM<\/p>\n
$ R\r\n> install.packages(\"VGAM\")\r\n> q(save=\"no\")<\/pre>\n
5. \u4f7f\u7528Quake\u7684bin\u76ee\u5f55\u4e0b\u7684quake.py\u6765\u8fd0\u884c\u7a0b\u5e8f<\/p>\n
\u4e09. quake\u7684\u4f7f\u7528\u53c2\u6570<\/h1>\n
1. \u4e3b\u8981\u53c2\u6570\uff1a<\/p>\n
-r READSF<\/span>\r\n    Fastq\u6587\u4ef6\u540d\r\n-f READS_LISTF<\/span>\r\n    \u4e00\u4e2a\u6587\u4ef6\uff0c\u5176\u4e2d\u5305\u542bfastq\u6587\u4ef6\u540d\uff0c\u6bcf\u884c\u4e00\u4e2a\u6587\u4ef6\u540d\uff1b\u5982\u679c\u662f\u53cc\u672b\u7aefreads\uff0c\u5219\u662f\u4e00\u884c\u4e24\r\n\u4e2a\u6587\u4ef6\u540d\r\n-k K<\/span>\r\n    \u4f7f\u7528\u7684k-mer\u7684\u957f\u5ea6\u3002\u5982\u679c\u57fa\u56e0\u7ec4\u5927\u5c0f\u4e3aG\uff0c\u5219k-mer\u957f\u5ea6\u9009\u62e9\u4e3a: k ~= log(200G)\r\n\/log(4)\r\n-p PROC  default: 4<\/span>\r\n    \u4f7f\u7528\u7684CPU\u7ebf\u7a0b\u6570\r\n-q QUALITY_SCALE<\/span>\r\n    \u4f7f\u7528\u7684\u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\uff0c\u4e00\u822c\u662f64\u621633.\u5982\u679c\u4e0d\u7ed9\u51fa\uff0c\u5219\u8f6f\u4ef6\u4f1a\u81ea\u884c\u731c\u6d4b<\/pre>\n
2. \u8ba1\u7b97k-mer\u53c2\u6570\uff1a<\/p>\n
--no_jelly<\/span>\r\n    \u4f7f\u7528quake\u81ea\u5e26\u7684\u4e00\u4e2a\u7b80\u5355\u7684\u7a0b\u5e8f\u6765\u8fdb\u884ck-mer\u8ba1\u6570\uff0c\u800c\u4e0d\u662f\u4f7f\u7528jellyfish\u3002\u8be5\u7a0b\u5e8f\r\n\u662f\u5355\u7ebf\u7a0b\u8fd0\u884c\uff0c\u901f\u5ea6\u76f8\u5bf9\u6162\uff0c\u80fd\u6ee1\u8db3\u50cf\u5fae\u751f\u7269\u57fa\u56e0\u7ec4\u8fd9\u6837\u7684\u5c0f\u57fa\u56e0\u7ec4\u6d4b\u5e8f\uff0c\u4f46\u662f\u4e0d\u9002\u5408\u4e8e\u5927\u7684\u57fa\r\n\u56e0\u7ec4\u3002\r\n--no_count  default: false<\/span>\r\n    \u4e0d\u8fdb\u884ck-mer\u8ba1\u6570\uff0c\u800c\u5176\u8ba1\u6570\u7ed3\u679c\u5df2\u7ecf\u5b58\u4e8e\u5728\u76ee\u6807\u6587\u4ef6[readsfile].qcts\u548c[reads\r\nfile].cts\u4e2d\u4e86\u3002\r\n--int  default:false<\/span>\r\n    \u5bf9kmers\u4ee5\u6574\u6570\u7684\u65b9\u5f0f\u8fdb\u884c\u8ba1\u6570\uff0c\u800c\u4e0d\u4f7f\u7528\u78b1\u57fa\u8d28\u91cf\u503c\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u662f\u5229\u7528\u5230\u4e86\u78b1\u57fa\u8d28\u91cf\uff0c\r\n\u8ba1\u6570\u7684\u79f0\u4e3aqmer\u3002\r\n--hash_size=HASH_SIZE<\/span>\r\n    Jellyfish\u7684\u53c2\u6570\uff0c\u7528\u6765\u8bbe\u7f6eHash\u7684\u5927\u5c0f\u3002\u5982\u679c\u4e0d\u8bbe\u7f6e\uff0cQuake\u5219\u4f1a\u4f7f\u7528k\u6765\u4f30\u8ba1\u51fa\u4e00\r\n\u4e2a\u503c\u6765\u3002<\/pre>\n
3. \u8986\u76d6\u5ea6\u6a21\u578b\u53c2\u6570\uff1a<\/p>\n
--no_cut  default: false<\/span>\r\n    Quake\u4f7f\u7528k-mer\u8ba1\u6570\u6765\u753b\u76f4\u65b9\u56fe\uff0c\u901a\u8fc7\u8c03\u7528R\u811a\u672ccov_model_qmer.r<\/em>\u6765\u753b\u76f4\u65b9\u56fe\uff0c\u5e76\r\n\u51b3\u5b9a\u51faCoverage cutoff\u7684\u9608\u503c\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u662f\u6700\u4f18\u5316\u7684\u6a21\u578b\uff0c\u4ece\u800c\u5f97\u51fa\u4e00\u4e2acutoff\u7684Co\r\nverage\u503c\uff0c\u6b64\u503c\u5c06\u8f93\u51fa\u5230\u6587\u4ef6cutoff.txt\u4e2d\u3002\r\n--ratio=RATIO<\/span>\r\n    \u786e\u5b9aCoverage cutoff\u503c\u7684\u65f6\u5019\uff0c\u8be5\u503c\u5904\u5bf9\u5e94\u7684qmer\u9519\u8bef\u7684\u53ef\u80fd\u6027\u662f\u6b63\u786e\u7684\u53ef\u80fd\u6027\u7684\r\n\u500d\u6570(\u9ed8\u8ba4\u662f200\u500d)\uff0c\u5373\u6b63\u786e\u7387\u4e0d\u8db30.5%\u3002\u8be5\u503c\u8d8a\u5c0f\uff0c\u5219\u9608\u503c\u8d8a\u677e\u3002<\/pre>\n
4. reads\u7684\u4fee\u6b63\u53c2\u6570\uff1a<\/p>\n
-l MIN_READ<\/span>\r\n    \u8f93\u51fa\u7684\u957f\u5ea6>=\u6b64\u503c\u7684\u4fee\u6b63\u540e\u7684reads\u3002\u5f88\u591areads\u7531\u4e8e\u4fee\u6b63\u6216\u4fee\u526a\u540e\u4f1a\u8f83\u77ed\r\n--headers<\/span>\r\n    \u8f93\u51fa\u7684fastq\u6587\u4ef6\u4f7f\u7528\u7684\u5934\u548c\u539f\u59cb\u6587\u4ef6\u4e00\u81f4\uff0c\u4e0d\u5305\u542b\u4fee\u6b63\u4fe1\u606f\r\n--log<\/span>\r\n    \u8f93\u51fa\u4e00\u4e2alog\u6587\u4ef6\uff0c\u91cc\u9762\u5305\u542b\u6240\u6709\u7684\u4fee\u6b63\u65e5\u5fd7\uff0c\u5305\u62ec\"\u78b1\u57fa\u8d28\u91cf \u4f4d\u7f6e \u65b0\u7684\u78b1\u57fa \u65e7\u7684\u78b1\u57fa\"\u3002<\/pre>\n
\u56db. Quake\u7684\u7ed3\u679c<\/h1>\n
\u4f7f\u7528Quake\u5bf9\u53cc\u672b\u7aef\u6d4b\u5e8f\u6587\u4ef6 A.fastq \u548c B.fastq \u8fdb\u884creads\u4fee\u6b63\uff0c\u5219\u4ea7\u751f\u5982\u4e0b\u7ed3\u679c\u6587\u4ef6\uff1a<\/p>\n
A.cor.fastq  B.cor.fastq<\/span>\r\n    \u4fee\u6b63\u8fc7\u540e\u7684reads\u6587\u4ef6               \r\nA.cor_single.fastq  B.err_single.fastq<\/span>\r\n    A\u6587\u4ef6\u4e2d\u4fee\u6b63\u8fc7\u540e\u7684reads\u7ed3\u679c\uff1b\u800cB\u6587\u4ef6\u4e2d\u7684\u5e8f\u5217\u5219\u662ferror reads\r\nA.err_single.fastq  A.cor_single.fastq<\/span>\r\n    B\u6587\u4ef6\u4e2d\u4fee\u6b63\u8fc7\u540e\u7684reads\u7ed3\u679c\uff1b\u800cA\u6587\u4ef6\u4e2d\u7684\u5e8f\u5217\u5219\u662ferror reads\r\nA.err.fastq  B.err.fastq<\/span>\r\n    A\u548cB\u6587\u4ef6\u4e2d\u6210\u5bf9\u7684reads\u90fd\u662ferror reads<\/pre>\n
\u4e94. Quake\u7684correct\u7a0b\u5e8f<\/h1>\n
Quake\u7684bin\u6587\u4ef6\u4e2d\u6709\u4e00\u652fC++\u7684\u7a0b\u5e8f\uff0c\u7528\u4e8ereads\u7684\u4fee\u6b63\u3002\u5176\u5b9eQuake.py\u5728\u8fd0\u884c\u8fc7\u7a0b\u4f1a\u8c03\u7528\u8be5\u7a0b\u5e8f\uff0c\u4f46\u662f\u5f53\u51fa\u73b0\u57fa\u56e0\u7ec4\u8986\u76d6\u5ea6\u8f83\u4f4e\uff0c\u800ccutoff\u7684\u503c\u51fa\u73b0\u5f02\u5e38\u7ed3\u679c\uff0c\u6bd4\u5982\u5c0f\u4e8e1\u65f6\uff0c\u53ef\u4ee5\u8003\u8651\u4f7f\u7528\u8be5\u7a0b\u5e8f\u6765\u91cd\u65b0\u5bf9reads\u8fdb\u884c\u4fee\u6b63\uff0c\u53d6cutoff\u503c\u4e3a1.0\u3002\u5176\u4f7f\u7528\u65b9\u6cd5\u4e3a\uff1a<\/p>\n
$ correct -f [fastq list file] -k [k-mer size] -c [cutoff] -m [counts file] -p 24<\/pre>\n","protected":false},"excerpt":{"rendered":"
\u4e00. Quake\u7b80\u4ecb Quake\u662f\u7531CBCB(Center for Bioinf … \u7ee7\u7eed\u9605\u8bfb →<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[3],"tags":[39,41,38],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/819"}],"collection":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=819"}],"version-history":[{"count":18,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/819\/revisions"}],"predecessor-version":[{"id":829,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/819\/revisions\/829"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=819"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=819"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=819"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}