{"id":1389,"date":"2013-06-05T09:19:14","date_gmt":"2013-06-05T01:19:14","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1389"},"modified":"2013-06-07T19:21:44","modified_gmt":"2013-06-07T11:21:44","slug":"%e4%bd%bf%e7%94%a8crossbow%e4%bd%9c%e9%87%8d%e6%b5%8b%e5%ba%8f%e6%95%b0%e6%8d%ae%e7%9a%84snp%e5%88%86%e6%9e%90","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1389","title":{"rendered":"\u4f7f\u7528Crossbow\u4f5cSNP\u5206\u6790"},"content":{"rendered":"

Crossbow\uff1ahttp:\/\/bowtie-bio.sourceforge.net\/crossbow\/index.shtml<\/a><\/p>\n

\u5728\u8fd9\u91cc\u8bb2\u8ff0\u672c\u5730\u5316\u4f7f\u7528single computer\u8fd0\u884cCrossbow\u7684\u547d\u4ee4\u8be6\u89e3\u548c\u6d41\u7a0b\u3002<\/p>\n

1. Crossbow\u7684\u5b89\u88c5<\/h2>\n

\u5728\u4e0a\u9762\u63d0\u5230\u7684Crossbow\u4e3b\u9875\u4e0a\u70b9\u51fb\u4e0b\u8f7d\u94fe\u63a5\u53bbsourceforge\u4e0a\u4e0b\u8f7dCrossbow\u7684\u538b\u7f29\u5305\uff0c\u89e3\u538b\u5373\u53ef\u3002<\/p>\n

Crossbow\u7684\u4f7f\u7528\u9700\u8981\u4f9d\u8d56\u4e8ebowtie\u548csoapsnp\u3002\u5f53\u4f7f\u7528sra\u6570\u636e\u7684\u65f6\u5019\uff0c\u8fd8\u9700\u8981\u4f9d\u8d56\u4e8eSRA toolkit\u4e2d\u7684fastq-dump\u547d\u4ee4\u3002<\/p>\n

$ wget http:\/\/kaz.dl.sourceforge.net\/project\/bowtie-bio\/crossbow\/1.2.1\/crossbow-1.2.1.zip\r\n$ unzip crossbow-1.2.1.zip\r\n$ cd crossbow-1.2.1\/soapsnp\r\n$ make\r\n$ sudo cp soapsnp \/usr\/local\/bin\/\r\n$ cd ..\r\n$ .\/cb_local --test<\/pre>\n
cb_local\u662f\u672c\u5730\u5316\u7684Crossbow\u8fd0\u884c\u547d\u4ee4\uff0c–test\u7528\u4e8e\u68c0\u6d4b bowtie, soapsnp \u548c fastq-dump \u8fd9\u4e09\u4e2a\u7a0b\u5e8f\u662f\u5426\u80fd\u6b63\u5e38\u4f7f\u7528\u3002<\/p>\n
2. cb_local \u547d\u4ee4\u4e3b\u8981\u53c2\u6570<\/h2>\n
Crossbow\u53ef\u4ee5\u8fd0\u884c\u5728Amazon Elastic MapReduce (EMR)\u4e0a\uff0c\u5e94\u8be5\u662f\u6309\u8ba1\u7b97\u91cf\u6536\u8d39\uff1b\u4e5f\u53ef\u4ee5\u8fd0\u884c\u5728\u8ba1\u7b97\u673a\u96c6\u7fa4\u4e0a\uff1b\u6216\u8fd0\u884c\u5728\u5355\u4e2a\u7684\u8ba1\u7b97\u673a\u4e0a\u3002\u5176cb_local\u7279\u6709\u7684\u53c2\u6570\u6709\uff1a<\/p>\n
--reference <path><\/span>\r\n    \u53c2\u8003\u5e8f\u5217\u7684\u6587\u4ef6\u5939\u3002\u8be5\u6587\u4ef6\u5939\u7531\u4e00\u4e2a\u53c2\u8003\u5e8f\u5217jar\u6587\u4ef6\u4f7f\u7528unzip\u89e3\u538b\u7f29\u51fa\u6765\u7684\uff0c\u91cc\u9762\u4e3b\r\n\u8981\u5305\u62ec3\u4e2a\u5b50\u6587\u4ef6\u5939\u548c\u4e00\u4e2a\u5217\u8868\u6587\u4ef6\uff1a1.\"index\":\u91cc\u9762\u5305\u542bbowtie-bulid\u4ea7\u751f\u7684index\u6587\r\n\u4ef6\uff1b2.\"sequences\":\u91cc\u9762\u5305\u542b\u53c2\u8003\u5e8f\u5217\uff1b3.\"snps\":\u5df2\u6709\u7684\u53c2\u8003snp\u7ed3\u679c\uff1b4.\"cmap.\r\ntxt\":\u53c2\u8003\u5e8f\u540d\u548c\u5bf9\u5e94\u7684sequences\u6587\u4ef6\u5939\u4e2d\u7684fasta\u7684header\u540d\u5404\u5360\u4e00\u5217\u3002\r\n\r\n--input <path><\/span>\r\n\u8f93\u5165\u7684\u6587\u4ef6\u6216\u6587\u4ef6\u5939\u8def\u5f84\u3002\u5982\u679c\u4e0d\u6307\u5b9a--preprocess \u53c2\u6570\uff0c\u5219\u8be5\u53c2\u6570\u540e\u63a5\u7684\u662f\u4e00\u4e2a\r\n\u6587\u4ef6\u5939\uff0c\u8be5\u6587\u4ef6\u5939\u5305\u542b\u4e86reads\u7684\u9884\u5904\u7406\u7ed3\u679c\uff0c\u5373 --preprocess-output \u7684\u8f93\u51fa\u7ed3\u679c\uff1b\r\n\u5982\u679c\u6307\u5b9a\u4e86 --preprocess \u6216 --just-preprocess \u53c2\u6570\uff0c\u5219\u662f\u4e00\u4e2a\u6587\u672c\u6587\u4ef6\uff0c\u5185\u5bb9\r\n\u4e3a\u8f93\u5165\u7684\u5e8f\u5217\u6587\u4ef6\u7684\u4e00\u4e2a\u6e05\u5355(Labeled manifest files)\u3002\u8be5\u6587\u4ef6\u63cf\u8ff0\u4e86\u8f93\u5165\u5e8f\u5217\u6587\u4ef6\r\n\u548c\u6837\u672c\u7684\u4fe1\u606f\u3002\u5e8f\u5217\u6587\u4ef6\u662fFASTQ\u6216sra\u683c\u5f0f\u6587\u4ef6\uff0cFASTQ\u683c\u5f0f\u53ef\u4ee5\u662fgzip\u6216bzip2\u538b\u7f29\u3002\r\n\u8be5\u6587\u4ef6\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u4e2a\u6d4b\u5e8f\u7684\u7ed3\u679c\uff0c\u662f\u4ee5\u4e0b\u662f unpaired reads \u548c paired reads \u7684\r\n\u4e66\u5199\u65b9\u6cd5\uff1a\r\n<URL>(tab)<Optional MD5>\r\n<URL-1>(tab)<Optional MD5>(tab)<URL-2>(tab)<Optional MD5>\r\n\r\n\u5176\u4e2dURL\u662f\u6d4b\u5e8f\u7ed3\u679c\u6587\u4ef6\u7684\u8def\u5f84\uff0c\u53ef\u4ee5\u662fftp\u7ad9\u70b9\u4e0a\u7684\u6587\u4ef6\uff1bMD5\u662f\u53ef\u9009\u7684\uff0c\u4ee5\u5229\u4e8e\u4e0b\u8f7d\u6587\u4ef6\u540e\r\n\u7528\u4e8e\u6587\u4ef6\u7684\u5b8c\u6574\u5ea6\u68c0\u9a8c\uff0c\u82e5\u4e0d\u60f3\u8fdb\u884c\u68c0\u9a8c\uff0c\u5219\u8bbe\u7f6e\u4e3a0.\r\n\r\n--output <path><\/span>\r\n\u8f93\u51fa\u6587\u4ef6\u7684\u8def\u5f84\u3002\u5982\u679c --just-preprocess \u53c2\u6570\u7ed9\u5b9a\uff0c\u5219\u53ea\u662f\u5bf9reads\u6587\u4ef6\u8fdb\u884c\u9884\r\n\u5904\u7406\uff0c\u7ed9\u51fa\u7ed3\u679c\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\uff0c\u5219\u662f\u8f93\u51fa\u6700\u7ec8\u7ed3\u679c: \u7531SOAPsnp\u5bf9\u6bcf\u4e2a\u53c2\u8003\u5e8f\u5217\u8fdb\u884cSNP calls\r\n\u7684\u8ba1\u7b97\u7ed3\u679c\u3002\r\n\r\n--intermediate <path> default: \/tmp\/myrna\/intermediate\/<PID><\/span>\r\n\u4e2d\u95f4\u7ed3\u679c\u6587\u4ef6\u5b58\u653e\u7684\u4e34\u65f6\u8def\u5f84\u3002\u5982\u679c\u6307\u5b9a\u4e86 --keep-intermediates \u6216 --keep-\r\nall\u53c2\u6570\uff0c\u5219\u8be5\u6587\u4ef6\u5219\u4f1a\u4e00\u76f4\u5b58\u5728\u3002\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u4f1a\u4f7f\u7528\u5b8c\u6bd5\u540e\u5220\u9664\u3002\r\n\r\n--preprocess-output <path><\/span>\r\n\u5bf9reads\u8fdb\u884c\u9884\u5904\u7406\u7684\u8f93\u51fa\u8def\u5f84\u3002\u7531\u4e8e\u5bf9reads\u7684\u9884\u5904\u7406\u4f1a\u6d88\u8017\u5f88\u591a\u65f6\u95f4\uff0c\u56e0\u6b64\u4fdd\u7559\u6570\u636e\r\n\u7684\u9884\u5904\u7406\u7ed3\u679c\uff0c\u5bf9\u518d\u6b21\u8fd0\u884c\u7a0b\u5e8f\u6765\u8bf4\uff0c\u53ef\u4ee5\u8282\u7ea6\u5f88\u591a\u65f6\u95f4\u3002\r\n\r\n--keep-intermediates <path><\/span>\r\n\u4fdd\u7559\u7a0b\u5e8f\u8fd0\u884c\u4e2d\u751f\u6210\u7684\u7ed3\u679c\u6587\u4ef6\u5939\u548c\u6587\u4ef6\uff0c\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u8fd9\u4e9b\u6587\u4ef6\u4f1a\u88ab\u5c3d\u5feb\u7684\u81ea\u52a8\u5220\u9664\u3002\r\n\r\n--keep-all<\/span><\/span>\r\n\u4fdd\u7559\u6240\u6709\u7684\u4e34\u65f6\u6587\u4ef6\uff0c\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u8fd9\u4e9b\u6587\u4ef6\u4f1a\u88ab\u5c3d\u5feb\u7684\u81ea\u52a8\u5220\u9664\u3002\r\n\r\n--cpus <int> default: 1<\/span>\r\n\u8bbe\u5b9a\u7a0b\u5e8f\u8fd0\u884c\u4f7f\u7528\u7684CPU\u7ebf\u7a0b\u6570\u3002\r\n\r\n--bowtie <path><\/span>\r\n\u00a0 \u00a0 \u8bbe\u5b9abowtie\u7684\u8def\u5f84\r\n\r\n--fastq-dump <path><\/span>\r\n\u00a0 \u00a0 sra toolkit\u4e2dfastq-dump\u7684\u8def\u5f84\r\n\r\n--soapsnp <path><\/span>\r\n\u00a0 \u00a0 SOAPsnp\u7684\u8def\u5f84<\/pre>\n
\u4ee5\u4e0a\u8f93\u5165\u53c2\u6570\u6709\u4e2a\u6ce8\u610f\u4e8b\u9879\uff1a \u5f53 –input \u53c2\u6570\u7684\u8f93\u5165\u4e3a\u4e00\u4e2amanifest\u6587\u4ef6\u65f6\uff0c\u6587\u4ef6\u4e2d\u6307\u5411\u67d0\u4e00\u4e2afastq\u6216sra\u6587\u4ef6\u7684 URL \u5fc5\u987b\u662f\u7edd\u5bf9\u8def\u5f84\uff1b\u5982\u679c\u662f\u76f8\u5bf9\u8def\u5f84\u5219\u4f1a\u62a5\u9519\u3002<\/p>\n
\u5728EMR\u3001Hadoop\u548clocal\u4e0a\u4f7f\u7528Crossbow\u5171\u6709\u7684\u53c2\u6570\u5982\u4e0b\uff1a<\/p>\n
--quality { phred33 | phred64 | solexa64 }  default: phred33<\/span>\r\n    \u8bbe\u7f6e\u8f93\u5165reads\u7684\u78b1\u57fa\u8d28\u91cf\u683c\u5f0f\u3002phred33:\u8f93\u5165\u7684\u78b1\u57fa\u8d28\u91cf\u7b49\u4e8eASCII\u7801\u503c\u52a0\u4e0a33;\u6700\r\n\u4f4e\u78b1\u57fa\u8d28\u91cf\u662f\u201c#\u201d. phred64:\u8f93\u5165\u7684\u78b1\u57fa\u8d28\u91cf\u7b49\u4e8eASCII\u7801\u503c\u52a0\u4e0a64;\u6700\u4f4e\u78b1\u57fa\u8d28\u91cf\u662f\u201cB\u201d.\r\n\r\n--preprocess<\/span>\r\n    \u5f53 --input \u7684\u53c2\u6570\u662f\u4e00\u4e2a\u6587\u672c\u6587\u4ef6\uff08\u542b\u6709\u8f93\u5165\u5e8f\u5217\u4fe1\u606f\u7684\u6e05\u5355\uff09\u65f6\uff0c\u5219\u5fc5\u987b\u52a0\u5165\u8be5\u53c2\u6570\r\n\uff1b\u8be5\u53c2\u6570\u6307\u5b9a\u51fa\u4e86\u6587\u672c\u6587\u4ef6\u4e2d\u7684\u5e8f\u5217\u4fe1\u606f\u6765\uff0cCrossbow\u5219\u8fdb\u884c\u8fd9\u4e9breads\u7684\u9884\u5904\u7406\uff0c\u5c06\u751f\u6210\u7684\u9884\u5904\r\n\u7406reads\u7ed3\u679c\u8f93\u51fa\u5230 --preprocess-output \u6307\u5b9a\u7684\u6587\u4ef6\u5939\uff1b\u5982\u679c\u4e0d\u6307\u5b9a--preprocess\r\n-output\u53c2\u6570\uff0c\u5219\u8f93\u51fa\u5230 --intermediate \u6307\u5b9a\u7684\u6587\u4ef6\u5939\u3002\r\n\r\n--just-preprocess<\/span>\r\n    \u548c --preprocess \u53c2\u6570\u7c7b\u4f3c\uff0c\u4f46\u4e0d\u540c\u7684\u662f\u8fdb\u884creads\u9884\u5904\u7406\u540e\uff0c\u5373\u505c\u6b62pipeline\u7684\r\n\u8fd0\u884c\uff0c\u5e76\u5c06\u7ed3\u679c\u8f93\u51fa\u5230 --output\u6307\u5b9a\u7684\u6587\u4ef6\u5939\u3002\r\n\r\n--just-align<\/span>\r\n    \u4e0d\u5c06Myrna\u7684pipeline\u8fd0\u884c\u5230\u5e95\uff0c\u53ea\u662f\u8fd0\u884c\u5230\u6bd4\u5bf9\u7ed3\u675f\uff0c\u5e76\u5c06\u7ed3\u679c\u5b58\u653e\u5230 --output \r\n\u53c2\u6570\u6307\u5b9a\u7684URL.\r\n\r\n--resume-align<\/span>\r\n    \u4f7f\u7528\u6b64\u547d\u4ee4\u6765\u8fd0\u884c\u4e0a\u4e00\u4e2a\u547d\u4ee4\uff08\u6bd4\u5bf9\u5b8c\u6bd5\uff09\u8fc7\u540e\u7684\u9636\u6bb5\u3002 \u6b64\u65f6 --input \u7684\u53c2\u6570\u5219\u662f\u4e0a\r\n\u4e00\u4e2a\u547d\u4ee4\u4e2d --output\u7684URL\r\n\r\n--bowtie-args \"<args>\"  default: -m 1<\/span>\r\n    \u8bbe\u7f6ebowtie\u7684\u53c2\u6570\u3002\u70b9\u51fb\u67e5\u770bBowtie manual<\/a>\r\n\r\n--discard-reads <fraction>  default: 0.0<\/span>\r\n    \u4e22\u5f03\u4e00\u5b9a\u6bd4\u4f8b\u8f93\u7684reads\u6765\u8fdb\u884c\u7a0b\u5e8f\u7684\u8fd0\u884c\u3002\u6bd4\u5982 0.5 \u5219\u4ee3\u8868\u4e22\u5f0350%\u7684reads\u3002\u8be5\u53c2\r\n\u6570\u5e94\u7528\u4e8e\u6240\u6709\u8f93\u5165\u7684reads\u3002\u5bf9\u4e8e\u7a0b\u5e8f\u7684\u8c03\u8bd5\u6bd4\u8f83\u6709\u7528\u3002\r\n\r\n--discard-ref-bins <fraction> default:0.0<\/span>\r\n\u00a0 \u00a0 \u5728\u8fdb\u884cSNP calling\u4e4b\u524d\uff0c\u4e22\u5f03\u4e00\u5b9a\u6bd4\u4f8b\u7684\u53c2\u8003\u5e8f\u5217\uff0c\u518d\u8fdb\u884cSNP calling\u3002\u6709\u5229\u4e8e\r\ndebugging\u3002\r\n\r\n--discard-all <fraction><\/span>\r\n\u00a0 \u00a0 \u7b49\u540c\u4e8e\u5c06\u4e0a\u4e24\u4e2a\u53c2\u6570\u540c\u65f6\u8bbe\u5b9a\u5230\u8be5\u503c\u3002\r\n\r\n--soapsnp-args \"<args>\" \u00a0default: -2 -u -n -q<\/span>\r\n\u00a0 \u00a0 \u8bbe\u7f6eSOAPsnp\u7684\u53c2\u6570\u3002\u70b9\u51fb\u67e5\u770bSOAPsnp manual<\/a>\r\n\r\n--soapsnp-hap-args \"<args>\" \u00a0default: -r 0.0001<\/span>\r\n\u00a0 \u00a0 \u5bf9\u5355\u6838\u4f53\u6d4b\u5e8f\u6570\u636e\u8bbe\u7f6e\u7684\u53c2\u6570\r\n\r\n--soapsnp-dip-args \"<args>\" \u00a0default: -r 0.00005 -e 0.0001<\/span>\r\n\u00a0 \u00a0 \u5bf9\u53cc\u6838\u4f53\u6d4b\u5e8f\u6570\u636e\u8bbe\u7f6e\u7684\u53c2\u6570\r\n\r\n--haploids <chromosome-list><\/span>\r\n\u00a0 \u00a0 \u540e\u63a5\u9017\u53f7\u5206\u5f00\u7684\u53c2\u8003\u5e8f\u5217\u540d\u3002\u8fd9\u4e9b\u5e8f\u5217\u5728\u8fd0\u7528SOAPsnp\u8fdb\u884cSNP calling\u7684\u65f6\u5019\u6309\r\nhapolid\u8fdb\u884c\u5904\u7406\uff0c\u5176\u4f59\u7684\u5219\u6309diploid\u8fdb\u884c\u5904\u7406\u3002\u9ed8\u8ba4\u4e0b\u6240\u6709\u7684\u53c2\u8003\u5e8f\u5217\u90fd\u662f\u6309diploid\r\n\u5904\u7406\r\n\r\n--all-haploids<\/span>\r\n\u00a0 \u00a0 \u8bbe\u5b9a\u8be5\u53c2\u6570\uff0c\u8868\u660e\u5728\u4f7f\u7528SOAPsnp\u7684\u65f6\u5019\u6240\u6709\u7684\u53c2\u8003\u5e8f\u5217\u90fd\u6309hapolid\u8fdb\u884c\u5904\u7406\u3002\r\n\r\n--partition-len <int> default: 1,000,000<\/span>\r\n\u00a0 \u00a0 The bin size to use when binning alignments into partitions\r\nprior to SNP calling. If load imbalance occurrs in the SNP \r\ncalling step (some tasks taking far longer than others), try \r\ndecreasing this.\r\n\r\n--dry-run<\/span>\r\n\u00a0 \u00a0 Just generate a script containing the commands needed to \r\nlaunch the job, but don't run it. The script's location will be \r\nprinted so that you may run it later.\r\n\r\n--test<\/span>\r\n\u00a0 \u00a0 \u641c\u7d22Crossbow\u9700\u8981\u7684\u5de5\u5177(bowtie,SOAPsnp\u548cfastq-dump),\u6765\u68c0\u6d4bCrossbow\r\n\u80fd\u5426\u6b63\u5e38\u8fd0\u884c\r\n\r\n--tempdir `<path>` default: \/tmp\/Crossbow\/invoke.scripts<\/span>\r\n\u00a0 \u00a0 Local directory where temporary files (e.g. dynamically \r\ngenerated scripts) should be deposited.<\/pre>\n
3. \u8f93\u5165\u7684reference jar\u6587\u4ef6\u914d\u7f6e<\/h2>\n
\u8be5jar\u6587\u4ef6\u4f7f\u7528unzip\u89e3\u538b\u540e\uff0c\u5305\u62ec3\u4e2a\u6587\u4ef6\u5939\u548c1\u4e2a\u6587\u4ef6\uff0c\u5177\u4f53\u5982\u4e0b\uff1a<\/p>\n
1. sequences \u6587\u4ef6\u5939\uff1a \u8be5\u6587\u4ef6\u5939\u4e2d\u5305\u542b\u5f88\u591afasta\u6587\u4ef6\u3002fasta\u6587\u4ef6\u7684\u53d6\u540d\u4e00\u5b9a\u8981\u6309 chrX.fa \u6765\u4f5c\u4e3a\u6587\u4ef6\u540d\uff0c\u5176\u4e2d X \u662f\u4ece0\u5f00\u59cb\u7684\u8fde\u7eed\u7684\u6570\u5b57\uff1b\u6bcf\u4e2afasta\u6587\u4ef6\u4e2d\u53ea\u542b\u6709\u4e00\u6761\u5e8f\u5217\uff0cfasta\u6587\u4ef6\u7684header\u547d\u540d\u5fc5\u987b\u4e3a X.
\n2. cmap.txt \u6587\u4ef6\uff1a\u8be5\u6587\u4ef6\u8bb0\u5f55\u7740\u53c2\u8003\u5e8f\u5217\u7684\u771f\u5b9e\u540d\u79f0\u548c\u5176\u5bf9\u5e94\u7740\u7684\u6570\u5b57\u3002\u7b2c\u4e00\u5217\u4e3a\u53c2\u8003\u5e8f\u5217\u540d\uff0c\u7b2c\u4e8c\u5217\u4e3a\u6570\u5b57\uff1b\u4e2d\u95f4\u4f7f\u7528tab\u5206\u9694\u3002
\n3. index \u6587\u4ef6\u5939\uff1a\u4f7f\u7528bowtie-build\u5c06sequences\u4e2d\u7684\u6240\u6709\u7684fasta\u6587\u4ef6\u6784\u5efa\u4e00\u4e2a\u7d22\u5f15\uff0c\u5e76\u4e14\u7d22\u5f15\u6587\u4ef6\u7684\u524d\u7f00\u5fc5\u987b\u4e3a index\uff1b\u5e76\u4e14\u7d22\u5f15\u7684\u987a\u5e8f\u5fc5\u987b\u6309\u6570\u5b57\u7684id\u8fdb\u884c\u6392\u5e8f\u3002
\n4. snps \u6587\u4ef6\u5939\uff1a\u5982\u679c\u6709\u5df2\u77e5\u7684snp\u7ed3\u679c\uff0c\u653e\u7f6e\u5728\u6b64\u6587\u4ef6\u5939\u4e0b\uff1bSNP \u7ed3\u679c\u7684\u6587\u4ef6\u540d\u5fc5\u987b\u548c sequences \u6587\u4ef6\u5939\u4e0b\u7684 FASTA \u6587\u4ef6\u7684\u524d\u7f00\u4e00\u81f4\uff0c\u5e76\u52a0\u4e0a\u540e\u7f00 .snps. \u6bd4\u5982 chrX.snps\u3002SNP\u7ed3\u679c\u6587\u4ef6\u7684\u683c\u5f0f\u4e3a\u6587\u672c\u6587\u4ef6\uff0c\u5305\u542b\u7531tab\u5206\u9694\u768410\u5217\u5185\u5bb9\u3002<\/p>\n
\r\n1. \u53c2\u8003\u5e8f\u5217\u540d\r\n2. 1-based \u4f4d\u7f6e\r\n3. SNP\u662f\u5426\u6709\u9891\u7387\u4fe1\u606f(1 = yes, 0 = no)\r\n4. SNP\u662f\u5426\u6709\u5b9e\u9a8c\u9a8c\u8bc1(1 = yes, 0 = no)\r\n5. SNP\u662f\u5426\u5b9e\u9645\u662findel(1 = yes, 0 = no)\r\n6. A allele\u7684\u9891\u7387\r\n7. C allele\u7684\u9891\u7387\r\n8. T allele\u7684\u9891\u7387\r\n9. G allele\u7684\u9891\u7387\r\n10. SNP id\r\n<\/pre>\n
\u5c06\u4e0a\u8ff0\u6587\u4ef6\u548c\u95ee\u5939\u5c31\u51c6\u5907\u597d\u540e\uff0c\u5373\u53ef\u6253\u5305\u6210jar\u6587\u4ef6\u3002<\/p>\n
\r\n$ jar cf ref-XXX.jar sequences snps index cmap.txt\r\n<\/pre>\n
4. Crossbow\u8fd0\u884c\u8fc7\u7a0b\u548c\u7ed3\u679c<\/h2>\n
Crossbow\u8fd0\u884c\u67094\u6b65\uff0c\u5206\u522b\u662f\uff1a<\/p>\n
1. \u5bf9reads\u8fdb\u884c\u9884\u5904\u7406\u3002\u901a\u8fc7$CrossbowHome\/Copy.pl\u8fdb\u884creads\u7684\u9884\u5904\u7406\u3002
\n2. \u8fdb\u884c\u5e8f\u5217\u7684\u6bd4\u5bf9\u3002\u901a\u8fc7$CrossbowHome\/Align.pl\u8c03\u7528bowtie\u6765\u8fdb\u884c\u5e8f\u5217\u6bd4\u5bf9\u3002
\n3. \u8fdb\u884cSNPs Calling\u3002\u901a\u8fc7$CrossbowHome\/Soapsnp.pl\u8c03\u7528soapsnp\u6765Call SNPs\u3002
\n4. \u540e\u5904\u7406\u3002\u901a\u8fc7$CrossbowHome\/CBFinish.pl\u6765\u5904\u7406\u7ed3\u679c\uff0c\u4f7f\u7ed3\u679c\u548c\u539f\u59cb\u7684\u53c2\u8003\u5e8f\u5217\u540d\u4e00\u81f4\u3002<\/p>\n
Crossbow\u5f97\u5230\u7684\u7ed3\u679c\u5728 –output \u53c2\u6570\u8bbe\u7f6e\u7684\u6587\u4ef6\u5939\u7684 crossbow_results \u5b50\u6587\u4ef6\u5939\u4e2d\u3002\u6bcf\u4e2a\u53c2\u8003\u5e8f\u5217\u5f97\u5230\u4e00\u4e2a\u4f7f\u7528gzip\u538b\u7f29\u540e\u7684\u7ed3\u679c\u3002\u6bd4\u5982\uff1a
\n\/crossbow_results\/chr1.gz
\n\/crossbow_results\/chr2.gz
\n\/crossbow_results\/chr3.gz<\/p>\n
\u6bcf\u4e00\u4e2a\u6587\u4ef6\u5305\u542b\u7740SOAPsnp\u683c\u5f0f\u7684SNPs\uff0c\u6bcf\u884c\u8bb0\u5f55\u4e00\u4e2aSNP\u3002\u8be5SOAPsnp\u683c\u5f0f\u7684\u5305\u62ec18\u5217\uff0c\u5176\u610f\u4e49\u5982\u4e0b\uff1a<\/p>\n
\r\n1. \u53c2\u8003\u5e8f\u5217\u540d\r\n2. 1-based\u4f4d\u7f6e\r\n3. \u53c2\u8003\u5e8f\u5217\u7684\u57fa\u56e0\u578b\r\n4. \u6837\u54c1\u7684\u57fa\u56e0\u578b\r\n5. \u6837\u54c1\u57fa\u56e0\u578b\u7684\u8d28\u91cf\u5206\u6570\r\n6. \u6700\u4f18\u7684\u78b1\u57fa\r\n7. \u6700\u4f18\u78b1\u57fa\u7684\u5e73\u5747\u78b1\u57fa\u8d28\u91cf\r\n8. \u552f\u4e00\u6bd4\u5bf9\u5230\u8be5\u4f4d\u70b9\u7684\u5bf9\u5e94\u7740\u6700\u4f18\u78b1\u57fa\u7684reads\u6570\r\n9. \u6240\u6709\u6bd4\u5bf9\u5230\u8be5\u4f4d\u70b9\u7684\u5bf9\u5e94\u7740\u6700\u4f18\u78b1\u57fa\u7684reads\u6570\r\n10. \u6b21\u4f18\u78b1\u57fa\r\n11. \u6b21\u4f18\u78b1\u57fa\u7684\u5e73\u5747\u78b1\u57fa\u8d28\u91cf\r\n12. \u552f\u4e00\u6bd4\u5bf9\u5230\u8be5\u4f4d\u70b9\u7684\u5bf9\u5e94\u7740\u6b21\u4f18\u78b1\u57fa\u7684reads\u6570\r\n13. \u6240\u6709\u6bd4\u5bf9\u5230\u8be5\u4f4d\u70b9\u7684\u5bf9\u5e94\u7740\u6b21\u4f18\u78b1\u57fa\u7684reads\u6570\r\n14. \u8be5\u4f4d\u70b9\u7684\u6d4b\u5e8f\u6df1\u5ea6\r\n15. \u8be5\u4f4d\u70b9\u5bf9\u5e94\u7740paired\u6bd4\u5bf9\u7684\u6d4b\u5e8f\u6df1\u5ea6\r\n16. Rank sum test P-value\r\n17. Average copy number of nearby region\r\n18. \u8be5\u4f4d\u70b9\u662f\u5426\u662f\u4e00\u4e2a\u5df2\u77e5\u7684SNP\uff08\u901a\u8fc7\u548c -s \u53c2\u6570\u4e2d\u6307\u5b9a\u6587\u4ef6\u7684\u5bf9\u6bd4)\r\n\r\n\u6ce8\u610f\uff1a \u7b2c15\u5217\u662fCrossbow\u5bf9SOAPsnp\u4fee\u9970\u540e\u624d\u6dfb\u52a0\u7684\u3002\r\n<\/pre>\n
5. \u70b9\u8bc4\uff1aCrossbow\u548csamtools\u8fdb\u884cSNPs calling<\/h2>\n
\u4e2a\u4eba\u901a\u8fc7\u4f7f\u7528\u4ee5\u4e0a\u4e24\u79cd\u8f6f\u4ef6\u5bf9\u5b9e\u9645\u6570\u636e\u7684\u8fd0\u7b97\u7ed3\u679c\uff0c\u53d1\u73b0\uff1asamtools\u6bd4Crossbow\u5f97\u5230\u7684\u7ed3\u679c\u8981\u597d\u3002\u8868\u73b0\u4e3a\u5982\u4e0b\u51e0\u70b9\uff1a<\/p>\n
1. \u8fd9\u4e24\u4e2a\u8f6f\u4ef6\u90fd\u662f\u4f7f\u7528bowtie\u8fdb\u884c\u7684\u6bd4\u5bf9\uff1b\u800cCrossbow\u662f\u4f7f\u7528SOAPsnp\u5bf9\u6bd4\u5bf9\u7ed3\u679c\u8fdb\u884cSNP calling\u3002\u800csamtools\u7ed3\u5408\u5176\u4e00\u8d77\u53d1\u5e03\u7684bcftools\u8fdb\u884cSNPs calling\u3002
\n2. \u901a\u8fc7samtool tview\u5bf9bowtie\u7684\u6bd4\u5bf9\u7ed3\u679c\u8fdb\u884c\u6d4f\u89c8\uff0c\u6765\u4eba\u5de5\u89c2\u5bdf\u5e76\u6bd4\u8f83\u8fd9\u4e24\u4e2a\u8f6f\u4ef6\u7684\u7ed9\u51fa\u7684\u7ed3\u679c\u3002\u53d1\u73b0samtools\u7684\u7ed3\u679c\u6bd4\u8f83\u6b63\u786e\u3002\u5f88\u591a\u5728samtools tview\u4e2d\u660e\u663e\u663e\u793a\u4e3aSNP\u7684\u786e\u5728Crossbow\u4e2d\u6ca1\u6709\u7ed9\u51fa\uff1b\u4f46\u662f\uff0c\u4e00\u4e9bmap\u8d28\u91cf\u5f88\u5dee\uff0c\u6216\u6bd4\u5bf9\u4e0a\u6570\u76ee\u5f88\u5c11\u7684SNPs\u5374\u53ea\u5728Crossbow\u4e2d\u7ed9\u51fa\u3002
\n3. Crossbow\u53ea\u80fd\u8fdb\u884cSNPs calling\uff0c\u4e0d\u80fd\u8fdb\u884cIndels calling\u3002\u800csamtools\u5219\u80fd\u8fdb\u884cshort Indels calling\u3002
\n4. Crossbow\u4f7f\u7528bowtie\u4f5c\u4e3a\u6bd4\u5bf9\u8f6f\u4ef6\uff1b\u800csamtools\u5219\u53ef\u4ee5\u8fd0\u7528bowtie2\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002<\/p>\n
\u7efc\u4e0a\uff0c\u53ef\u4ee5\u4f18\u5148\u8003\u8651\u4f7f\u7528samtools\u6765\u8fdb\u884cSNP\u6216Indel\u7684calling\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
Crossbow\uff1ahttp:\/\/bowtie-bio.sourceforge.n … \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":[],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1389"}],"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=1389"}],"version-history":[{"count":14,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1389\/revisions"}],"predecessor-version":[{"id":1392,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1389\/revisions\/1392"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1389"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1389"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1389"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}