{"id":178,"date":"2012-08-28T15:44:08","date_gmt":"2012-08-28T07:44:08","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=178"},"modified":"2013-06-28T14:15:17","modified_gmt":"2013-06-28T06:15:17","slug":"bowtie2%e7%a5%a5%e8%a7%a3","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=178","title":{"rendered":"Bowtie2\u7528\u6cd5\u7965\u89e3"},"content":{"rendered":"

\u53c2\u8003\u81ea\uff1ahttp:\/\/bowtie-bio.sourceforge.net\/bowtie2\/manual.shtml<\/a><\/p>\n

\u61d2\u4eba\u5fc5\u770b<\/h1>\n
\u5bf9\u53c2\u8003\u5e8f\u5217\u6784\u5efaindex\r\n$ bowtie2-build genome.fasta index\r\n\r\n\u5c1d\u8bd5\u4f7f\u7528\u524d10000\u4e2areads\u8fdb\u884c\u6bd4\u5bf9\r\n$ bowtie2 -u 10000 -p 8 -x index -1 reads1.fq -2 reads2.fq -S out.sam\r\n\r\n\u4f7f\u75288\u4e2a\u7ebf\u7a0b\u8fdb\u884c\u6bd4\u5bf9\r\n$ bowtie2 -p 8 -x index -1 reads1.fq -2 reads2.fq -S out.sam\r\n\r\n\u6bd4\u5bf9\u7684sam\u7ed3\u679c\u4e2d\u6dfb\u52a0\u4e86read group\u4fe1\u606f\r\n$ bowtie2 -p 8 --rg-id sample01 --rg \"PL:ILLUMINA\" --rg \"SM:sample01\" -x index -1 reads1.fq -2 reads2.fq -S out.sam \r\n\r\n\u5e38\u7528\u7684\u53c2\u6570\u8fdb\u884c\u6bd4\u5bf9\uff0c\u53ef\u4ee5\u66f4\u6539\u5176\u4e2d\u7684\u53c2\u6570\u83b7\u5f97\u66f4\u597d\u7684\u7ed3\u679c\r\n$ bowtie2 -q --phred33 --sensitive --end-to-end -I 0 -X 500 --fr --un unpaired --al aligned --un-conc unconc --al-conc alconc -p 6 --reorder -x <bt2-idx> {-1 <m1gt; -2 <m2> | -U <r>} -S [<hit>]<\/pre>\n
\u7528\u6cd5\uff1a<\/h1>\n
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} -S [<hit>] <\/code><\/pre>\n
bowtie2-build\u7528\u6cd5<\/h1>\n
bowtie2-build\u9ed8\u8ba4\u60c5\u51b5\u4e0b\u5c06fasta\u6587\u4ef6\u6362\u6210index\u7684\u6570\u636e\u5e93\u3002\r\n$ bowtie2-build <fasta\u6587\u4ef6> <\u8981\u751f\u5b58\u7684\u7d22\u5f15\u6587\u4ef6\u524d\u7f00\u540d><\/pre>\n
\u5fc5\u987b\u53c2\u6570\uff1a<\/h1>\n
-x<\/span> <bt2-idx> <\/code><\/span>\u7531<\/code>bowtie2-build<\/code><\/span>\u6240\u751f\u6210\u7684\u7d22\u5f15\u6587\u4ef6\u7684\u524d\u7f00\u3002\u9996\u5148 \u5728\u5f53\u524d\u76ee\u5f55\u641c\u5bfb\uff0c\u7136\u540e<\/code>\r\n\u5728\u73af\u5883\u53d8\u91cf <\/code>BOWTIE2_INDEXES <\/code><\/span>\u4e2d\u5236\u5b9a\u7684\u6587\u4ef6\u5939\u4e2d\u641c\u5bfb\u3002<\/code>\r\n\r\n-1<\/span> <m1> <\/code><\/span>\u53cc\u672b\u7aef\u6d4b\u5bfb\u5bf9\u5e94\u7684\u6587\u4ef6<\/code>1<\/code><\/span>\u3002\u53ef\u4ee5\u4e3a\u591a\u4e2a\u6587\u4ef6\uff0c\u5e76\u7528\u9017\u53f7\u5206\u5f00\uff1b\u591a\u4e2a\u6587\u4ef6\u5fc5\u987b\u548c <\/code>-2 <\/code><\/span>\r\n<m2> <\/code><\/span>\u4e2d\u5236\u5b9a\u7684\u6587\u4ef6\u4e00\u4e00\u5bf9\u5e94\u3002\u6bd4\u5982<\/code>:\"-1 flyA_1.fq,flyB_1.fq -2 flyA_2.fq,flyB<\/code><\/span>\r\n_2.fq\". <\/code><\/span>\u6d4b\u5e8f\u6587\u4ef6\u4e2d\u7684<\/code>reads<\/code><\/span>\u7684\u957f\u5ea6\u53ef\u4ee5\u4e0d\u4e00\u6837\u3002<\/code>\r\n\r\n-2<\/span> <m2> <\/code><\/span>\u53cc\u672b\u7aef\u6d4b\u5bfb\u5bf9\u5e94\u7684\u6587\u4ef6<\/code>2.<\/span>\r\n\r\n-U<\/span> <r> <\/code><\/span>\u975e\u53cc\u672b\u7aef\u6d4b\u5bfb\u5bf9\u5e94\u7684\u6587\u4ef6\u3002\u53ef\u4ee5\u4e3a\u591a\u4e2a\u6587\u4ef6\uff0c\u5e76\u7528\u9017\u53f7\u5206\u5f00\u3002\u6d4b\u5e8f\u6587\u4ef6\u4e2d\u7684<\/code>reads<\/code><\/span>\u7684<\/code>\r\n\u957f\u5ea6\u53ef\u4ee5\u4e0d\u4e00\u6837\u3002<\/code>\r\n\r\n-S<\/span> <hit> <\/code><\/span>\u6240\u751f\u6210\u7684<\/code>SAM<\/code><\/span>\u683c\u5f0f\u7684\u6587\u4ef6\u524d\u7f00\u3002\u9ed8\u8ba4\u662f\u8f93\u5165\u5230\u6807\u51c6\u8f93\u51fa\u3002<\/code><\/pre>\n
\u4ee5\u4e0b\u662f\u53ef\u9009\u53c2\u6570\uff1a<\/h1>\n
\u8f93\u5165\u53c2\u6570<\/h2>\n
-q <\/code><\/span>\u8f93\u5165\u7684\u6587\u4ef6\u4e3a<\/code>FASTQ<\/code><\/span>\u683c\u5f0f\u6587\u4ef6\uff0c\u6b64\u9879\u4e3a\u9ed8\u8ba4\u503c\u3002<\/code>\r\n\r\n-qseq <\/code><\/span>\u8f93\u5165\u7684\u6587\u4ef6\u4e3a<\/code>QSEQ<\/code><\/span>\u683c\u5f0f\u6587\u4ef6\u3002<\/code>\r\n\r\n-f <\/code><\/span>\u8f93\u5165\u7684\u6587\u4ef6\u4e3a<\/code>FASTA<\/code><\/span>\u683c\u5f0f\u6587\u4ef6\u3002\u9009\u62e9\u6b64\u9879\u65f6\uff0c\u8868\u793a<\/code>--ignore-quals<\/code><\/span>\u4e5f\u88ab\u9009\u62e9\u4e86\u3002<\/code>\r\n\r\n-r <\/code><\/span>\u8f93\u5165\u7684\u6587\u4ef6\u4e2d\uff0c\u6bcf\u4e00\u884c\u4ee3\u8868\u4e00\u6761\u5e8f\u5217\uff0c\u6ca1\u6709\u5e8f\u5217\u540d\u548c\u6d4b\u5e8f\u8d28\u91cf\u7b49\u3002\u9009\u62e9\u6b64\u9879\u65f6\uff0c\u8868\u793a<\/code>--<\/code><\/span>\r\nignore-quals<\/code><\/span>\u4e5f\u88ab\u9009\u62e9\u4e86\u3002<\/code>\r\n\r\n-c<\/span> <\/code><\/span>\u540e\u76f4\u63a5\u4e3a\u6bd4\u5bf9\u7684<\/code>reads<\/code><\/span>\u5e8f\u5217\uff0c\u800c\u4e0d\u662f\u5305\u542b\u5e8f\u5217\u7684\u6587\u4ef6\u540d\u3002\u5e8f\u5217\u95f4\u7528\u9017\u53f7\u9694\u5f00\u3002\u9009\u62e9\u6b64\u9879\u65f6\uff0c<\/code>\r\n\u8868\u793a\u2014<\/code>ignore-quals<\/code><\/span>\u4e5f\u88ab\u9009\u62e9\u4e86\u3002<\/code>\r\n\r\n-s\/--skip <int><\/span> input<\/code><\/span>\u7684<\/code>reads<\/code><\/span>\u4e2d\uff0c\u8df3\u8fc7\u524d<\/code><int><\/code><\/span>\u4e2a<\/code>reads<\/code><\/span>\u6216\u8005<\/code>pairs<\/code><\/span>\u3002<\/code>\r\n\r\n-u\/--qupto <int> <\/code><\/span>\u53ea\u6bd4\u5bf9\u524d<\/code><int><\/code><\/span>\u4e2a<\/code>reads<\/code><\/span>\u6216\u8005<\/code>pairs<\/code><\/span>\uff08\u5728\u8df3\u8fc7\u524d<\/code><int><\/code><\/span>\u4e2a<\/code>reads<\/code><\/span>\u6216\u8005<\/code>\r\npairs<\/code><\/span>\u540e\uff09\u3002<\/code>Default: no limit.<\/code><\/span>\r\n\r\n-5\/--trim5 <int> <\/code><\/span>\u526a\u6389<\/code>5'<\/code><\/span>\u7aef<\/code><int><\/code><\/span>\u957f\u5ea6\u7684\u78b1\u57fa\uff0c\u518d\u7528\u4e8e\u6bd4\u5bf9\u3002<\/code>(default: 0).<\/code><\/span>\r\n\r\n-3\/--trim3 <int> <\/code><\/span>\u526a\u6389<\/code>3'<\/code><\/span>\u7aef<\/code><int><\/code><\/span>\u957f\u5ea6\u7684\u78b1\u57fa\uff0c\u518d\u7528\u4e8e\u6bd4\u5bf9\u3002<\/code>(default: 0).<\/code><\/span>\r\n\r\n--phred33 <\/code><\/span>\u8f93\u5165\u7684\u78b1\u57fa\u8d28\u91cf\u7b49\u4e8e<\/code>ASCII<\/code><\/span>\u7801\u503c\u52a0\u4e0a<\/code>33. <\/code><\/span>\u5728\u6700\u8fd1\u7684<\/code>illumina pipiline<\/code><\/span>\u4e2d<\/code>\r\n\u5f97\u4ee5\u8fd0\u7528\u3002<\/code>\u6700\u4f4e\u78b1\u57fa\u8d28\u91cf\u662f\u201c#\u201d\u3002\r\n\r\n--phred64 <\/code><\/span>\u8f93\u5165\u7684\u78b1\u57fa\u8d28\u91cf\u7b49\u4e8e<\/code>ASCII<\/code><\/span>\u7801\u503c\u52a0\u4e0a<\/code>64.<\/code><\/span>\u6700\u4f4e\u78b1\u57fa\u8d28\u91cf\u662f\u201cB\u201d\u3002\r\n\r\n--solexa-quals <\/code><\/span>\u5c06<\/code>Solexa<\/code><\/span>\u7684\u78b1\u57fa\u8d28\u91cf\u8f6c\u6362\u4e3a<\/code>Phred<\/code><\/span>\u3002\u5728\u8001\u7684<\/code>GA Pipeline<\/code><\/span>\u7248\u672c\u4e2d\u5f97\u4ee5<\/code>\r\n\u8fd0\u7528\u3002<\/code>Default: off.<\/code><\/span>\r\n --int-quals <\/code><\/span>\u8f93\u5165\u6587\u4ef6\u4e2d\u7684\u78b1\u57fa\u8d28\u91cf\u4e3a\u7528\u201c \u201d\u5206\u9694\u7684\u6570\u503c\uff0c\u800c\u4e0d\u662f<\/code>ASCII<\/code><\/span>\u7801\u3002\u6bd4\u5982 <\/code>40 40 <\/code><\/span>\r\n30 40...<\/code><\/span>\u3002<\/code>Default: off.<\/code><\/span><\/pre>\n
\u00a0–end-to-end\u6a21\u5f0f\u4e0b\u7684\u9884\u8bbe\u53c2\u6570<\/h2>\n
--very-fast<\/span><\/code><\/span> <\/code>Same as: -D 5 -R 1 -N 0 -L 22 -i S,0,2.50<\/span><\/code> <\/code><\/span>\r\n--fast<\/span><\/code><\/span> Same as: <\/span>-D 10 -R 2 -N 0 -L 22 -i S,0,2.50<\/span><\/code> <\/code><\/span>\r\n--sensitive <\/span><\/code><\/span>Same as: <\/span>-D 15 -R 2 -N 0 -L 22 -i S,1,1.15<\/span><\/code> (default in --<\/code><\/span>end-to-end <\/code>mode)<\/span> <\/code><\/span>\r\n--very-sensitive<\/span><\/code><\/span> Same as: <\/span>-D 20 -R 3 -N 0 -L 20 -i S,1,0.50<\/span><\/code><\/span><\/pre>\n
–loca\u6a21\u5f0f\u4e0b\u7684\u9884\u8bbe\u53c2\u6570<\/h2>\n
--very-fast-local<\/span><\/code><\/span> <\/code>Same as: -D 5 -R 1 -N 0 -L 25 -i S,1,2.00<\/span><\/code> <\/code><\/span>\r\n--fast-local<\/span><\/code><\/span> Same as: <\/span>-D 10 -R 2 -N 0 -L 22 -i S,1,1.75<\/span><\/code> <\/code><\/span>\r\n--sensitive-local<\/span><\/code><\/span> Same as: <\/span>-D 15 -R 2 -N 0 -L 20 -i S,1,0.75<\/span><\/code> (default in --local mode)<\/span> <\/code><\/span>\r\n--very-sensitive-local<\/span><\/code><\/span> Same as: <\/span>-D 20 -R 3 -N 0 -L 20 -i S,1,0.50<\/span><\/code><\/span><\/pre>\n
\u00a0\u6bd4\u5bf9\u53c2\u6570\uff1a<\/h2>\n
-N <int> <\/code><\/span>\u8fdb\u884c\u79cd\u5b50\u6bd4\u5bf9\u65f6\u5141\u8bb8\u7684<\/code>mismatch<\/code><\/span>\u6570<\/code>. <\/code><\/span>\u53ef\u4ee5\u8bbe\u4e3a<\/code>0<\/code><\/span>\u6216\u8005<\/code>1. <\/code>Default: 0.<\/span>\r\n\r\n-L <int> <\/code><\/span>\u8bbe\u5b9a\u79cd\u5b50\u7684\u957f\u5ea6<\/code>.<\/code><\/span>\r\n\r\n************************************************************<\/code><\/span>\r\n\u529f\u80fd\u9009\u9879\r\n\u7ed9bowtie<\/span>\u7684\u4e00\u4e9b\u53c2\u6570\u8bbe\u5b9a\u503c\u7684\u65f6\u5019\uff0c\u4f7f\u7528\u4e00\u4e2a\u8ba1\u7b97\u516c\u5f0f\u4ee3\u66ff\uff0c\u4e8e\u662f\u503c\u7684\u5927\u5c0f\u4e0e\u6bd4\u5bf9\u5e8f\u5217\u7684\u957f\r\n\u5ea6\u6210\u4e00\u5b9a\u5173\u7cfb\u3002<func><\/code><\/span>\u6709\u4e09\u90e8\u5206\u7ec4\u6210<\/code>: (a)<\/code><\/span>\u8ba1\u7b97\u65b9\u6cd5<\/code>, <\/code><\/span>\u5305\u62ec\u5e38\u6570<\/code>(C),<\/code><\/span>\u7ebf\u6027<\/code>(L),<\/code><\/span>\u5e73\u65b9\u6839<\/code>(S)<\/code><\/span>\u548c<\/code>\r\n\u81ea\u7136\u5bf9\u6570<\/code>(G); (b)<\/code><\/span>\u4e00\u4e2a\u5e38\u6570<\/code>; (c)<\/code><\/span>\u4e00\u4e2a\u7cfb\u6570<\/code>. <\/code><\/span>\r\n\u4f8b\u5982<\/code>: <\/code><\/span>\r\n<func> <\/code><\/span>\u4e3a <\/code>L,-0.4,-0.6 <\/code><\/span>\u5219\u8ba1\u7b97\u516c\u5f0f\u4e3a<\/code>: f(x) = -0.4 + -0.6 * x<\/code><\/span>\r\n<func> <\/span>\u4e3aG,1,5.4 <\/code><\/span>\u5219\u8ba1\u7b97\u516c\u5f0f\u4e3a<\/code>: f(x) = 1.0 + 5.4 * ln(x)<\/code><\/span>\r\n************************************************************<\/code><\/span>\r\n\r\n-i <func> <\/code><\/span>\u8bbe\u5b9a\u4e24\u4e2a\u76f8\u90bb\u79cd\u5b50\u95f4\u6240\u95f4\u8ddd\u7684\u78b1\u57fa\u6570\u3002<\/code>\r\n************************************************************<\/code><\/span>\r\n\u4f8b\u5982\uff1a\u5982\u679c<\/code>read<\/code><\/span>\u7684\u957f\u5ea6\u4e3a<\/code>30, <\/code><\/span>\u79cd\u5b50\u7684\u957f\u5ea6\u4e3a<\/code>10, <\/code><\/span>\u76f8\u90bb\u79cd\u5b50\u7684\u95f4\u8ddd\u4e3a<\/code>6,<\/code><\/span>\u5219\u63d0\u53d6\u51fa\u7684\u79cd\u5b50\u5982\u4e0b<\/code>\r\n\u6240\u793a\uff1a<\/code>\r\nRead: \u00a0 \u00a0 \u00a0TAGCTACGCTCTACGCTATCATGCATAAAC<\/code><\/span>\r\nSeed 1 fw: TAGCTACGCT<\/code><\/span>\r\nSeed 1 rc: AGCGTAGCTA<\/code><\/span>\r\nSeed 2 fw: \u00a0 \u00a0 \u00a0 CGCTCTACGC<\/code><\/span>\r\nSeed 2 rc: \u00a0 \u00a0 \u00a0 GCGTAGAGCG<\/code><\/span>\r\nSeed 3 fw: \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 ACGCTATCAT<\/code><\/span>\r\nSeed 3 rc: \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 ATGATAGCGT<\/code><\/span>\r\nSeed 4 fw: \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 TCATGCATAA<\/code><\/span>\r\nSeed 4 rc: \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 TTATGCATGA <\/code><\/span>\r\n************************************************************<\/code><\/span>\r\n <\/code>\u5728<\/code>--end-to-end<\/code><\/span>\u6a21\u5f0f\u4e2d\u9ed8\u8ba4\u503c\u4e3a\u201d<\/code>-i S,1,1.15\u201d.<\/code><\/span>\u5373\u8868\u793a<\/code>f(x) = 1 + 1.15 * <\/code><\/span>\r\nsqrt(x). <\/code><\/span>\u5982\u679c<\/code>read<\/code><\/span>\u957f\u5ea6\u4e3a<\/code>100, <\/code><\/span>\u5219\u76f8\u90bb\u79cd\u5b50\u7684\u95f4\u8ddd\u4e3a<\/code>12.<\/code><\/span>\r\n\r\n--n-ceil <func> <\/code><\/span>\u8bbe\u5b9a<\/code>read<\/code><\/span>\u4e2d\u5141\u8bb8\u542b\u6709\u4e0d\u786e\u5b9a\u78b1\u57fa<\/code>(<\/code><\/span>\u975e<\/code>GTAC,<\/code><\/span>\u901a\u5e38\u4e3a<\/code>N)<\/code><\/span>\u7684\u6700\u5927\u6570\u76ee<\/code>. <\/code><\/span>\r\nDefault: L,0,0.15. <\/code><\/span>\u8ba1\u7b97\u516c\u5f0f\u4e3a<\/code>: f(x) = 0 + 0.15 * x, <\/code><\/span>\u8868\u793a\u957f\u5ea6\u4e3a<\/code>100<\/code><\/span>\u7684<\/code>read<\/code><\/span>\r\n\u6700\u591a\u8fd0\u884c\u5b58\u5728<\/code>15<\/code><\/span>\u4e2a\u4e0d\u786e\u5b9a\u78b1\u57fa<\/code>. <\/code><\/span>\u4e00\u65e6\u4e0d\u786e\u5b9a\u78b1\u57fa\u6570\u8d85\u8fc7<\/code>15, <\/code><\/span>\u5219\u8be5\u6761<\/code>read<\/code><\/span>\u4f1a\u88ab\u8fc7\u6ee4\u6389<\/code>.<\/code><\/span>\r\n\r\n--dpad <int><\/span> Default: 15.<\/code><\/span>\r\n\r\n--gbar <int> <\/code><\/span>\u5728<\/code>read<\/code><\/span>\u5934\u5c3e<\/code><int><\/code><\/span>\u4e2a\u78b1\u57fa\u5185\u4e0d\u5141\u8bb8<\/code>gap. Default: 4.<\/code><\/span>\r\n --ignore-quals <\/code><\/span>\u8ba1\u7b97\u9519\u914d\u7f5a\u5206\u7684\u65f6\u5019\u4e0d\u8003\u8651\u78b1\u57fa\u8d28\u91cf<\/code>. <\/code><\/span>\u5f53\u8f93\u5165\u5e8f\u5217\u7684\u6a21\u5f0f\u4e3a<\/code>-f, -r <\/code><\/span>\u6216<\/code>\r\n\u8005<\/code>-c<\/code><\/span>\u7684\u65f6\u5019<\/code>, <\/code><\/span>\u8be5\u8bbe\u7f6e\u81ea\u52a8\u6210\u4e3a\u9ed8\u8ba4\u8bbe\u7f6e<\/code>.<\/code><\/span>\r\n\r\n--nofw\/--norc<\/span> \u2013nofw<\/code><\/span>\u8bbe\u5b9a<\/code>read<\/code><\/span>\u4e0d\u548c\u524d\u5bfc\u94fe<\/code>(forward reference strand)<\/code><\/span>\u8fdb\u884c\u6bd4\u5bf9<\/code>;<\/code><\/span>\r\n <\/code>--norc<\/code><\/span>\u8bbe\u5b9a\u4e0d\u548c\u540e\u968f\u94fe<\/code>(reverse-complement reference strand)<\/code><\/span>\u8fdb\u884c\u6bd4\u5bf9<\/code>. <\/code><\/span>\r\nDefault: both strands enabled.<\/code><\/span>\r\n\r\n--end-to-end <\/code><\/span>\u6bd4\u5bf9\u662f\u5c06\u6574\u4e2a<\/code>read<\/code><\/span>\u548c\u53c2\u8003\u5e8f\u5217\u8fdb\u884c\u6bd4\u5bf9<\/code>. <\/code><\/span>\u8be5\u6a21\u5f0f<\/code>--ma<\/code><\/span>\u7684\u503c\u4e3a<\/code>0. <\/code><\/span>\u8be5\u6a21\u5f0f\u4e3a<\/code>\r\n\u9ed8\u8ba4\u6a21\u5f0f<\/code>, --local<\/code><\/span>\u6a21\u5f0f\u51b2\u7a81<\/code>.<\/code><\/span>\r\n\r\n--local <\/code><\/span>\u8be5\u6a21\u5f0f\u4e0b\u5bf9<\/code>read<\/code><\/span>\u8fdb\u884c\u5c40\u90e8\u6bd4\u5bf9<\/code>, <\/code><\/span>\u4ece\u800c<\/code>, read<\/code><\/span>\u4e24\u7aef\u7684\u4e00\u4e9b\u78b1\u57fa\u4e0d\u6bd4\u5bf9\uff0c\u4ece\u800c\u4f7f\u6bd4<\/code>\r\n\u5bf9\u5f97\u5206\u6ee1\u8db3\u8981\u6c42<\/code>. <\/code><\/span>\u8be5\u6a21\u5f0f\u4e0b \u2013<\/code>ma<\/code><\/span>\u9ed8\u8ba4\u4e3a<\/code>2.<\/code><\/span><\/pre>\n
\u00a0\u5f97\u5206\u7f5a\u5206\u53c2\u6570<\/h2>\n
--ma <int> <\/code><\/span>\u8bbe\u5b9a\u5339\u914d\u5f97\u5206<\/code>. --local<\/code><\/span>\u6a21\u5f0f\u4e0b\u6bcf\u4e2a<\/code>read<\/code><\/span>\u4e0a\u78b1\u57fa\u548c\u53c2\u8003\u5e8f\u5217\u4e0a\u78b1\u57fa\u5339\u914d<\/code>, <\/code><\/span>\u5219<\/code>\r\n\u52a0<\/code><int><\/code><\/span>\u5206<\/code>. <\/code><\/span>\u5728\u2014<\/code>end-to-end<\/code><\/span>\u6a21\u5f0f\u4e2d\u65e0\u6548<\/code>. Default: 2.<\/code><\/span>\r\n\r\n--mp MX,MN <\/code><\/span>\u8bbe\u5b9a\u9519\u914d\u7f5a\u5206<\/code>. <\/code><\/span>\u5176\u4e2d<\/code>MX<\/code><\/span>\u4e3a\u6240\u7f5a\u6700\u9ad8\u5206<\/code>, MN<\/code><\/span>\u4e3a\u6240\u7f5a\u6700\u4f4e\u5206<\/code>. <\/code><\/span>\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b\u7f5a\u5206\u4e0e<\/code>\r\n\u78b1\u57fa\u8d28\u91cf\u76f8\u5173<\/code>. <\/code><\/span>\u7f5a\u5206\u9075\u5faa\u7684\u516c\u5f0f\u4e3a<\/code>: MN + floor( (MX-MN)(MIN(Q, 40.0)\/40.0) ). <\/code><\/span>\r\n\u5176\u4e2d<\/code>Q<\/code><\/span>\u4e3a\u78b1\u57fa\u7684\u8d28\u91cf\u503c<\/code>. <\/code><\/span>\u5982\u679c\u8bbe\u7f6e\u4e86\u2014<\/code>ignore-qual<\/code><\/span>\u53c2\u6570<\/code>, <\/code><\/span>\u5219\u9519\u914d\u603b\u662f\u7f5a\u6700\u9ad8\u5206<\/code>. Default: <\/code><\/span>\r\nMX = 6, MN = 2.<\/code><\/span>\r\n\r\n--np <int> <\/code><\/span>\u5f53\u5339\u914d\u4f4d\u70b9\u4e2d<\/code>read, reference<\/code><\/span>\u4e0a\u6709\u4e0d\u786e\u5b9a\u78b1\u57fa<\/code>(<\/code><\/span>\u6bd4\u5982<\/code>N)<\/code><\/span>\u65f6\u6240\u8bbe\u5b9a\u7684\u7f5a\u5206\u503c<\/code>.<\/code><\/span>\r\nDefault: 1.<\/code><\/span>\r\n\r\n--rdg <int1>,<int2> <\/code><\/span>\u8bbe\u7f6e\u5728<\/code>read<\/code><\/span>\u4e0a\u6253\u5f00<\/code>gap <\/code><\/span>\u7f5a\u5206<\/code><int1>, <\/code><\/span>\u5ef6\u957f<\/code>gap<\/code><\/span>\u7f5a\u5206<\/code><int2>. <\/code><\/span>\r\nDefault: 5, 3.<\/code><\/span>\r\n\r\n--rfg <int1>,<int2> <\/code><\/span>\u8bbe\u7f6e\u5728<\/code>reference<\/code><\/span>\u4e0a\u6253\u5f00<\/code>gap <\/code><\/span>\u7f5a\u5206<\/code><int1>, <\/code><\/span>\u5ef6\u957f<\/code>gap<\/code><\/span>\u7f5a\u5206<\/code>\r\n<int2>. Default: 5, 3.<\/code><\/span>\r\n\r\n--score-min <func> <\/code><\/span>\u8bbe\u5b9a\u6210\u4e3a\u6709\u6548\u6bd4\u5bf9\u7684\u6700\u5c0f\u5206\u503c<\/code>. <\/code><\/span>\u5728\u2014<\/code>end-to-end<\/code><\/span>\u6a21\u5f0f\u4e0b\u9ed8\u8ba4\u503c\u4e3a<\/code>:<\/code><\/span>\r\nL,-0.6,-0.6; <\/code><\/span>\u5728<\/code>--local<\/code><\/span>\u6a21\u5f0f\u4e0b\u9ed8\u8ba4\u503c\u4e3a<\/code>: G,20,8.<\/code><\/span><\/pre>\n
\u62a5\u544a\u53c2\u6570<\/h2>\n
-k <int> <\/code><\/span>\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b<\/code>, bowtie2<\/code><\/span>\u641c\u7d22\u51fa\u4e86\u4e00\u4e2a<\/code>read<\/code><\/span>\u4e0d\u540c\u7684\u6bd4\u5bf9\u7ed3\u679c<\/code>, <\/code><\/span>\u5e76\u62a5\u544a\u5176\u4e2d\u6700\u597d\u7684<\/code>\r\n\u6bd4\u5bf9\u7ed3\u679c<\/code>(<\/code><\/span>\u5982\u679c\u597d\u51e0\u4e2a\u6700\u597d\u7684\u6bd4\u5bf9\u7ed3\u679c\u5f97\u5206\u4e00\u81f4<\/code>, <\/code><\/span>\u5219\u968f\u673a\u6311\u9009\u51fa\u5176\u4e2d\u4e00\u4e2a<\/code>). <\/code><\/span>\u800c\u5728\u8be5\u6a21\u5f0f\u4e0b<\/code>, <\/code><\/span>\r\nbowtie2<\/code><\/span>\u6700\u591a\u641c\u7d22\u51fa\u4e00\u4e2a<\/code>read <int><\/code><\/span>\u4e2a\u6bd4\u5bf9\u7ed3\u679c<\/code>, <\/code><\/span>\u5e76\u5c06\u8fd9\u4e9b\u7ed3\u679c\u6309\u5f97\u5206\u964d\u5e8f\u62a5\u544a\u51fa\u6765<\/code>.<\/code><\/span>\r\n\r\n-a <\/code><\/span>\u548c<\/code>-k<\/code><\/span>\u53c2\u6570\u4e00\u6837<\/code>, <\/code><\/span>\u4e0d\u8fc7\u4e0d\u9650\u5236\u641c\u7d22\u7684\u7ed3\u679c\u6570\u76ee<\/code>. <\/code><\/span>\u5e76\u5c06\u6240\u6709\u7684\u6bd4\u5bf9\u7ed3\u679c\u90fd\u6309\u964d\u5e8f\u62a5\u544a\u51fa\u6765<\/code>. <\/code><\/span>\r\n\u6b64\u53c2\u6570\u548c<\/code>-k<\/code><\/span>\u53c2\u6570\u51b2\u7a81<\/code>. <\/code><\/span>\u503c\u5f97\u6ce8\u610f\u7684\u662f<\/code>: <\/code><\/span>\u5982\u679c\u57fa\u56e0\u7ec4\u542b\u6709\u5f88\u591a\u91cd\u590d\u5e8f\u5217\u65f6<\/code>, <\/code><\/span>\u8be5\u53c2\u6570\u4f1a\u5bfc\u81f4\u7a0b\u5e8f<\/code>\r\n\u8fd0\u884c\u6781\u5176\u7f13\u6162<\/code>.<\/code><\/span><\/pre>\n
Effort \u53c2\u6570<\/h2>\n
-D <int> <\/code><\/span>\u6bd4\u5bf9\u65f6<\/code>, <\/code><\/span>\u5c06\u4e00\u4e2a\u79cd\u5b50\u5ef6\u957f\u540e\u5f97\u5230\u6bd4\u5bf9\u7ed3\u679c<\/code>, <\/code><\/span>\u5982\u679c\u4e0d\u4ea7\u751f\u66f4\u597d\u7684\u6216\u6b21\u597d\u7684\u6bd4\u5bf9\u7ed3\u679c<\/code>, <\/code><\/span>\r\n\u5219\u8be5\u6b21\u6bd4\u5bf9\u5931\u8d25<\/code>. <\/code><\/span>\u5f53\u5931\u8d25\u6b21\u6570\u8fde\u7eed\u8fbe\u5230<\/code><int><\/code><\/span>\u6b21\u540e<\/code>, <\/code><\/span>\u5219\u8be5\u6761<\/code>read<\/code><\/span>\u6bd4\u5bf9\u7ed3\u675f<\/code>. Bowtie2<\/code><\/span>\u624d\u4f1a<\/code>\r\n\u7ee7\u7eed\u8fdb\u884c\u4e0b\u53bb<\/code>. Default: 15. <\/code><\/span>\u5f53\u5177\u6709<\/code>-k<\/code><\/span>\u6216<\/code>-a<\/code><\/span>\u53c2\u6570<\/code>, <\/code><\/span>\u5219\u8be5\u53c2\u6570\u6240\u4ea7\u751f\u7684\u9650\u5236\u4f1a\u81ea\u52a8\u8c03\u6574<\/code>.<\/code><\/span>\r\n\r\n-R <int> <\/code><\/span>\u5982\u679c\u4e00\u4e2a<\/code>read<\/code><\/span>\u6240\u751f\u6210\u7684\u79cd\u5b50\u5728\u53c2\u8003\u5e8f\u5217\u4e0a\u5339\u914d\u4f4d\u70b9\u8fc7\u591a<\/code>. <\/code><\/span>\u5f53\u6bcf\u4e2a\u79cd\u5b50\u5e73\u5747\u5339\u914d\u8d85<\/code>\r\n\u8fc7<\/code>300<\/code><\/span>\u4e2a\u4f4d\u7f6e<\/code>, <\/code><\/span>\u5219\u901a\u8fc7\u4e00\u4e2a\u4e0d\u540c\u7684\u504f\u79fb\u6765\u91cd\u65b0\u751f\u6210\u79cd\u5b50\u8fdb\u884c\u6bd4\u5bf9<\/code>. <int><\/code><\/span>\u5219\u662f\u91cd\u65b0\u751f\u6210\u79cd\u5b50<\/code>\r\n\u7684\u6b21\u6570<\/code>. Default: 2.<\/code><\/span><\/pre>\n
Paired-end \u53c2\u6570<\/h2>\n
-I\/--minins <int> <\/span><\/code><\/span>\u8bbe\u5b9a\u6700\u5c0f\u7684\u63d2\u5165\u7247\u6bb5\u957f\u5ea6<\/code>. Default: 0.<\/span><\/code><\/span>\r\n\r\n-X\/--maxins <int> <\/span><\/code><\/span>\u8bbe\u5b9a\u6700\u957f\u7684\u63d2\u5165\u7247\u6bb5\u957f\u5ea6<\/code>. Default: 500.<\/span><\/code><\/span>\r\n\r\n--fr\/--rf\/--ff <\/span><\/code><\/span>\u8bbe\u5b9a\u4e0a\u4e0b\u6e38<\/code>reads<\/span><\/code><\/span>\u548c\u524d\u5bfc\u94fe<\/code>paired-end<\/span><\/code><\/span>\u6bd4\u5bf9\u7684\u65b9\u5411<\/code>. --fr: <\/span><\/code><\/span>\u5339\u914d\u65f6\uff0c<\/code>\r\nread1<\/span><\/code><\/span>\u5728<\/code>5'<\/span><\/code><\/span>\u7aef\u4e0a\u6e38<\/code>, <\/span><\/code><\/span>\u548c\u524d\u5bfc\u94fe\u4e00\u81f4<\/code>, read2<\/span><\/code><\/span>\u5728<\/code>3'<\/span><\/code><\/span>\u4e0b\u6e38<\/code>, <\/span><\/code><\/span>\u548c\u524d\u5bfc\u94fe\u53cd\u5411\u4e92\u8865<\/code>. <\/span><\/code><\/span>\u6216\u8005<\/code>read2<\/span><\/code><\/span>\u5728<\/code>\r\n\u4e0a\u6e38<\/code>, read1<\/span><\/code><\/span>\u5728\u4e0b\u6e38\u53cd\u5411\u4e92\u8865<\/code>; --rf: read1<\/span><\/code><\/span>\u5728<\/code>5'<\/span><\/code><\/span>\u7aef\u4e0a\u6e38<\/code>, <\/span><\/code><\/span>\u548c\u524d\u5bfc\u94fe\u53cd\u5411\u4e92\u8865<\/code>, read2<\/span><\/code><\/span>\u5728<\/code>\r\n3'<\/span><\/code><\/span>\u7aef\u4e0b\u6e38<\/code>, <\/span><\/code><\/span>\u548c\u524d\u5bfc\u94fe\u4e00\u81f4<\/code>; --ff: <\/span><\/code><\/span>\u4e24\u6761<\/code>reads<\/span><\/code><\/span>\u90fd\u548c\u524d\u5bfc\u94fe\u4e00\u81f4<\/code>. Default: --fr. <\/span><\/code><\/span>\u9ed8\u8ba4<\/code>\r\n\u8bbe\u7f6e\u9002\u5408\u4e8e<\/code>Illumina<\/span><\/code><\/span>\u7684<\/code>paired-end<\/span><\/code><\/span>\u6d4b\u5e8f\u6570\u636e<\/code>; <\/span><\/code><\/span>\u82e5\u662f<\/code>mate-paired, <\/span><\/code><\/span>\u5219\u8981\u9009\u62e9\u2014<\/code>rf<\/span><\/code><\/span>\u53c2\u6570<\/code>.<\/span><\/code><\/span>\r\n\r\n--no-mixed <\/span><\/code><\/span>\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b<\/code>, <\/span><\/code><\/span>\u4e00\u5bf9<\/code>reads<\/span><\/code><\/span>\u4e0d\u80fd\u6210\u5bf9\u6bd4\u5bf9\u5230\u53c2\u8003\u5e8f\u5217\u4e0a<\/code>, <\/span><\/code><\/span>\u5219\u5355\u72ec\u5bf9\u6bcf\u4e2a<\/code>read<\/span><\/code><\/span>\u8fdb<\/code>\r\n\u884c\u6bd4\u5bf9<\/code>. <\/span><\/code><\/span>\u8be5\u9009\u9879\u5219\u963b\u6b62\u6b64\u884c\u4e3a<\/code>.<\/span><\/code><\/span>\r\n\r\n--no-discordant <\/span><\/code><\/span>\u9ed8\u8ba4\u8bbe\u7f6e\u4e0b<\/code>, <\/span><\/code><\/span>\u4e00\u5bf9<\/code>reads<\/span><\/code><\/span>\u4e0d\u80fd\u548c\u8c10\u6bd4\u5bf9<\/code>(concordant alignment,<\/span><\/code><\/span>\r\n\u5373\u6ee1\u8db3<\/code>-I, -X, --fr\/--rf\/--ff<\/span><\/code><\/span>\u7684\u6761\u4ef6<\/code>)<\/span><\/code><\/span>\u5230\u53c2\u8003\u5e8f\u5217\u4e0a<\/code>, <\/span><\/code><\/span>\u5219\u641c\u5bfb\u5176\u4e0d\u548c\u8c10\u6bd4\u5bf9<\/code>(discon<\/span><\/code><\/span>\r\ncordant alignment, <\/span><\/code><\/span>\u5373\u4e24\u6761<\/code>reads<\/span><\/code><\/span>\u90fd\u80fd\u72ec\u4e00\u65e0\u4e8c\u5730\u6bd4\u5bf9\u5230\u53c2\u8003\u5e8f\u5217\u4e0a<\/code>, <\/span><\/code><\/span>\u4f46\u662f\u4e0d\u6ee1\u8db3<\/code>-I,<\/span><\/code><\/span>\r\n-X,--fr\/--rf\/--ff<\/span><\/code><\/span>\u7684\u6761\u4ef6<\/code>). <\/span><\/code><\/span>\u8be5\u9009\u9879\u963b\u6b62\u6b64\u884c\u4e3a<\/code>.<\/span><\/code><\/span>\r\n\r\n--dovetail<\/span> read1<\/span><\/code><\/span>\u548c<\/code>read2<\/span><\/code><\/span>\u7684\u5173\u7cfb\u4e3a<\/code>dovetail<\/span><\/code><\/span>\u7684\u65f6\u5019<\/code>,<\/span><\/code><\/span>\u8be5\u72b6\u51b5\u7b97\u4e3a\u548c\u8c10\u6bd4\u5bf9<\/code>. <\/span><\/code><\/span>\u9ed8\u8ba4\u60c5\u51b5<\/code>\r\n\u4e0b<\/code>dovetail<\/span><\/code><\/span>\u4e0d\u7b97\u548c\u8c10\u6bd4\u5bf9<\/code>.<\/span><\/code><\/span>\r\n\r\n--no-contain<\/span> read1<\/span><\/code><\/span>\u548c<\/code>read2<\/span><\/code><\/span>\u7684\u5173\u7cfb\u4e3a\u5305\u542b\u7684\u65f6\u5019<\/code>, <\/span><\/code><\/span>\u8be5\u72b6\u51b5\u4e0d\u7b97\u4e3a\u548c\u8c10\u6bd4\u5bf9<\/code>. <\/span><\/code><\/span>\u9ed8\u8ba4\u60c5\u51b5<\/code>\r\n\u4e0b\u5305\u542b\u5173\u7cfb\u7b97\u4e3a\u548c\u8c10\u6bd4\u5bf9<\/code>.<\/span><\/code><\/span>\r\n\r\n--no-overlap<\/span> read1<\/span><\/code><\/span>\u548c<\/code>read2<\/span><\/code><\/span>\u7684\u5173\u7cfb\u4e3a\u6709\u91cd\u53e0\u7684\u65f6\u5019<\/code>, <\/span><\/code><\/span>\u8be5\u72b6\u51b5\u4e0d\u7b97\u4e3a\u548c\u8c10\u6bd4\u5bf9<\/code>. <\/span><\/code><\/span>\u9ed8\u8ba4\u60c5<\/code>\r\n\u51b5\u4e0b\u4e24\u4e2a<\/code>reads<\/span><\/code><\/span>\u91cd\u53e0\u7b97\u4e3a\u548c\u8c10\u6bd4\u5bf9<\/code>.<\/span><\/code><\/span><\/pre>\n
\u8f93\u51fa\u53c2\u6570<\/h2>\n
-t\/--time <\/span><\/code> --un <path> <\/span><\/code><\/span>\u5c06<\/code>unpaired reads<\/span><\/code><\/span>\u5199\u5165\u5230<\/code><path>.<\/span><\/code><\/span>\r\n--un-gz <path> <\/span><\/code><\/span>\u5c06<\/code>unpaired reads<\/span><\/code><\/span>\u5199\u5165\u5230<\/code><path>, gzip<\/span><\/code><\/span>\u538b\u7f29<\/code>.<\/span><\/code><\/span>\r\n--un-bz2 <path> <\/span><\/code><\/span>\u5c06<\/code>unpaired reads<\/span><\/code><\/span>\u5199\u5165\u5230<\/code><path>, bz2<\/span><\/code><\/span>\u538b\u7f29<\/code>.<\/span><\/code><\/span>\r\n\r\n--al <path> <\/span><\/code><\/span>\u5c06\u81f3\u5c11\u80fd\u6bd4\u5bf9<\/code>1<\/span><\/code><\/span>\u6b21\u4ee5\u4e0a\u7684<\/code>unpaired reads<\/span><\/code><\/span>\u5199\u5165<\/code><path>.<\/span><\/code><\/span>\r\n--al-gz <path><\/span> ... ,gzip<\/span><\/code><\/span>\u538b\u7f29<\/code>.<\/span><\/code><\/span>\r\n--al-bz2 <path><\/span> ... ,bz2<\/span><\/code><\/span>\u538b\u7f29<\/code>.<\/span><\/code><\/span>\r\n\r\n--un-conc <path> <\/span><\/code><\/span>\u5c06\u4e0d\u80fd\u548c\u8c10\u6bd4\u5bf9\u7684<\/code>paired-end reads<\/span><\/code><\/span>\u5199\u5165<\/code><path>.<\/span><\/code><\/span>\r\n--un-conc-gz <path><\/span> ... ,gzip<\/span><\/code><\/span>\u538b\u7f29<\/code>.<\/span><\/code><\/span>\r\n--un-conc-bz2 <path><\/span> ... ,bz2<\/span><\/code><\/span>\u538b\u7f29<\/code>.<\/span><\/code><\/span>\r\n\r\n--al-conc <path><\/span> <\/span><\/code><\/span>\u5c06\u81f3\u5c11\u80fd\u548c\u8c10\u6bd4\u5bf9\u4e00\u6b21\u4ee5\u4e0a\u7684<\/code>paired-end reads<\/span><\/code><\/span>\u5199\u5165<\/code><path>.<\/span><\/code><\/span>\r\n--al-conc-gz <path><\/span> ... ,gzip<\/span><\/code><\/span>\u538b\u7f29<\/code>.<\/span><\/code><\/span>\r\n--al-conc-bz2 <path><\/span>... ,bz2<\/span><\/code><\/span>\u538b\u7f29<\/code>.<\/span><\/code><\/span>\r\n\r\n--quiet <\/span><\/span>\u5b89\u9759\u6a21\u5f0f,<\/span><\/span>\u9664\u4e86\u6bd4\u5bf9\u9519\u8bef\u548c\u4e00\u4e9b\u4e25\u91cd\u7684\u9519\u8bef, <\/span><\/span>\u4e0d\u5728\u5c4f\u5e55\u4e0a\u8f93\u51fa\u4efb\u4f55\u4e1c\u897f.<\/span><\/span>\r\n\r\n--met-file <path> <\/span><\/span>\u5c06bowtie2<\/span><\/span>\u7684\u68c0\u6d4b\u4fe1\u606f(metrics)<\/span><\/span>\u5199\u5165\u6587\u4ef6<path>. <\/span><\/span>\u7528\u4e8edebug. <\/span><\/span>\r\nDefault: metrics disabled.<\/span>\r\n\r\n--met-stderr <path> <\/span><\/code><\/span>\u5c06<\/code>bowtie2<\/span><\/code><\/span>\u7684\u68c0\u6d4b\u4fe1\u606f<\/code>(metrics)<\/span><\/code><\/span>\u5199\u5165\u6807\u51c6\u9519\u8bef\u6587\u4ef6\u53e5\u67c4<\/code>. <\/span><\/code><\/span>\u548c\u4e0a<\/code>\r\n\u4e00\u4e2a\u9009\u9879\u4e0d\u51b2\u7a81<\/code>. Default: metrics disabled.<\/span><\/code><\/span>\r\n\r\n--met <int> <\/span><\/code><\/span>\u6bcf\u9694<\/code><int><\/span><\/code><\/span>\u79d2\u5199\u5165\u4e00\u6b21<\/code>metrics<\/span><\/code><\/span>\u8bb0\u5f55<\/code>. Default: 1.<\/span><\/code><\/span><\/pre>\n
\u00a0Sam \u53c2\u6570<\/h2>\n
--no-unal <\/code><\/span>\u4e0d\u8bb0\u5f55\u6ca1\u6bd4\u5bf9\u4e0a\u7684<\/code>reads.<\/code><\/span>\r\n\r\n--no-hd <\/code><\/span>\u4e0d\u8bb0\u5f55<\/code>SAM header lines (<\/code><\/span>\u4ee5<\/code>@<\/code><\/span>\u5f00\u5934<\/code>).<\/code><\/span>\r\n\r\n--no-sq <\/code><\/span>\u4e0d\u8bb0\u5f55<\/code>@SQ<\/code><\/span>\u7684<\/code>SAM header lines.<\/code><\/span>\r\n\r\n--rg-id <text> <\/code><\/span>\u8bbe\u5b9a<\/code>read group ID\u4e3a<\/code><\/span>text\u3002\u5728SAM\u6587\u4ef6\u7684\u5934\u4e2d\u589e\u52a0\u4e00\u884c@RG\uff0c\u5728\u8f93\u51fa\u7684SAM\r\n\u6587\u4ef6\u4e2d\u6dfb\u52a0Tag \"RG:Z:text\"\u3002<\/code><\/span>\r\n\r\n--rg <text> <\/code><\/span>\u4f7f\u7528<\/code>text<\/code><\/span>\u4f5c\u4e3a@RG\u7684\u4e00\u5217\uff0c\u6bd4\u5982\"SM:Pool1\"<\/code>\u3002\u5728@RG\u4e2d\u52a0\u5165\u591a\u5217\uff0c\u5219\u591a\u6b21\u4f7f\u7528\r\n\u8be5\u53c2\u6570\u5373\u53ef\u3002\u5728\u8fdb\u884cVariant calling\u7684\u8fc7\u7a0b\u4e2d\u9700\u8981@RG\u5934\uff0cSM\u4fe1\u606f\u548cTag RG\u3002\r\n<\/code><\/span><\/pre>\n
\u6027\u80fd\u53c2\u6570<\/h2>\n
-o\/--offrate <int> <\/span><\/code><\/span>\u65e0\u89c6<\/code>index<\/span><\/code><\/span>\u7684<\/code>offrate<\/span><\/code><\/span>\u503c<\/code>, <\/span><\/code><\/span>\u4ee5<\/code><int><\/span><\/code><\/span>\u53d6\u4ee3\u4e4b<\/code>. Index<\/span><\/code><\/span>\u9ed8\u8ba4\u7684<\/code><int><\/span><\/code> <\/code><\/span>\r\n\u503c\u4e3a<\/code>5. <int><\/span><\/code><\/span>\u503c\u5fc5\u987b\u5927\u4e8e<\/code>index<\/span><\/code><\/span>\u7684<\/code>offrate<\/span><\/code><\/span>\u503c<\/code>, <\/span><\/code><\/span>\u540c\u65f6<\/code><int><\/span><\/code><\/span>\u8d8a\u5927<\/code>, <\/span><\/code><\/span>\u8017\u65f6\u8d8a\u957f\uff0c\u8017\u5185\u5b58\u8d8a\u5c11<\/code>.<\/span><\/code><\/span>\r\n\r\n-p\/--threads NTHREADS <\/span><\/code><\/span>\u8bbe\u7f6e\u7ebf\u7a0b\u6570<\/code>. Default: 1<\/span><\/code><\/span>\r\n\r\n--reorder <\/span><\/code><\/span>\u591a\u7ebf\u7a0b\u8fd0\u7b97\u65f6<\/code>, <\/span><\/code><\/span>\u6bd4\u5bf9\u7ed3\u679c\u5728\u987a\u5e8f\u4e0a\u4f1a\u548c\u6587\u4ef6\u4e2d<\/code>reads<\/span><\/code><\/span>\u7684\u987a\u5e8f\u4e0d\u4e00\u81f4<\/code>, <\/span><\/code><\/span>\u4f7f\u7528\u8be5\u9009<\/code>\r\n\u9879<\/code>, <\/span><\/code><\/span>\u5219\u4f7f\u5176\u4e00\u81f4<\/code>.<\/span><\/code><\/span>\r\n\r\n--mm <\/span><\/code><\/span>\u4f7f\u7528\u5185\u5b58\u5b9a\u4f4d\u7684<\/code>I\/O<\/span><\/code><\/span>\u6765\u8f7d\u5165<\/code>index, <\/span><\/code><\/span>\u800c\u4e0d\u662f\u5e38\u89c4\u7684\u6587\u4ef6<\/code>I\/O. <\/span><\/code><\/span>\u4ece\u800c\u4f7f\u591a\u4e2a<\/code>bowtie<\/span><\/code><\/span>\u7a0b<\/code>\r\n\u5e8f\u5171\u7528\u5185\u5b58\u4e2d\u540c\u6837\u7684<\/code>index, <\/span><\/code><\/span>\u8282\u7ea6\u5185\u5b58\u6d88\u8017<\/code>.<\/span><\/code><\/span><\/pre>\n
\u00a0\u5176\u5b83\u53c2\u6570\uff1a<\/h2>\n
--qc-filter<\/span> <\/span><\/code><\/span>\u6ee4\u9664<\/code>QSEQ fileter filed<\/span><\/code><\/span>\u4e3a\u975e<\/code>0<\/span><\/code><\/span>\u7684<\/code>reads. <\/span><\/code><\/span>\u4ec5\u5f53\u6709\u2014<\/code>qseq<\/span><\/code><\/span>\u9009\u9879\u65f6\u6709\u6548<\/code>. <\/span><\/code><\/span>\r\nDefault: off. <\/span><\/code><\/span>\r\n\r\n--seed <int> <\/code><\/span>\u4f7f\u7528<\/code><int><\/code><\/span>\u4f5c\u4e3a\u968f\u673a\u6570\u4ea7\u751f\u7684\u79cd\u5b50<\/code>. Default: 0.<\/code><\/span>\r\n\r\n--version<\/span> <\/code><\/span>\u6253\u5370\u7a0b\u5e8f\u7248\u672c\u5e76\u9000\u51fa<\/code>\r\n\r\n-h\/--help<\/code> <\/code><\/span>\u6253\u5370\u7528\u6cd5\u4fe1\u606f\u5e76\u63a8\u51fa<\/code><\/pre>\n

\n<\/code><\/p>\n","protected":false},"excerpt":{"rendered":"
\u53c2\u8003\u81ea\uff1ahttp:\/\/bowtie-bio.sourceforge.net\/bo … \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":[20],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/178"}],"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=178"}],"version-history":[{"count":57,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/178\/revisions"}],"predecessor-version":[{"id":1731,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/178\/revisions\/1731"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=178"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=178"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=178"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}