{"id":1325,"date":"2013-05-23T13:12:08","date_gmt":"2013-05-23T05:12:08","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1325"},"modified":"2013-10-30T22:01:27","modified_gmt":"2013-10-30T14:01:27","slug":"gbrowse%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=1325","title":{"rendered":"GBrowse\u7684\u5b89\u88c5\u548c\u4f7f\u7528"},"content":{"rendered":"

1. GBrowse\u7684\u5b89\u88c5<\/h1>\n

GBrowse\u5b89\u88c5\u8bf4\u660e\u6587\u6863\uff1ahttp:\/\/gmod.org\/wiki\/GBrowse_2.0_Install_HOWTO<\/a>
\nGBrowse\u7684\u5b89\u88c5\u5f88\u5c11\u6709\u80fd\u987a\u5229\u5b89\u88c5\u6210\u529f\u7684\u3002\u9700\u8981\u4e0d\u65ad\u7684\u6478\u7d22\uff0c\u770b\u6587\u6863\uff0c\u5e76\u641c\u7d22\u76f8\u5173\u9519\u8bef\uff0cgoogle\u770b\u522b\u4eba\u662f\u600e\u4e48\u89e3\u51b3\u7684\u3002\u6709\u7ba1\u4e00\u4e9b\u6211\u5b89\u88c5\u8fc7\u7a0b\u9047\u5230\u7684\u56f0\u96be\u5982\u4e0b\uff1a<\/p>\n

1.1 \u5b89\u88c5 io-lib<\/a>\u548cBio-SCF, io-lib\u662f\u5b89\u88c5Bio-SCF\u6240\u5fc5\u987b\u7684\u3002\u5728\u8fd9\u4e00\u6b65\u5bb9\u6613\u51fa\u95ee\u9898\uff0c\u5bfc\u81f4\u65e0\u6cd5\u5b89\u88c5\u3002<\/h2>\n
\r\n$ wget http:\/\/downloads.sourceforge.net\/project\/staden\/io_lib\/1.13.0\/io_lib-1.13.0.tar.gz\r\n$ make -j 8\r\n$ sudo make install\r\n\r\n$ wget http:\/\/search.cpan.org\/CPAN\/authors\/id\/L\/LD\/LDS\/Bio-SCF-1.03.tar.gz\r\n$ tar zxf Bio-SCF-1.03.tar.gz\r\n$ cd Bio-SCF-1.03\r\n$ perl Makefile.PL\r\n$ make\r\n$ sudo make install\r\n<\/pre>\n
1.2 \u5b89\u88c5Bio::Graphics<\/a><\/h2>\n
\u5f53\u4f7f\u7528CPAN\u5b89\u88c5\u7684\u65f6\u5019test\u9519\u8bef\uff0c\u4f7f\u7528\u624b\u5de5\u5b89\u88c5\uff0c\u4e0d\u7528\u8fdb\u884ctest\u3002<\/p>\n
2. Gbrowse\u7684\u914d\u7f6e<\/h1>\n
2.1 Gbrowse\u6587\u4ef6<\/h2>\n
\u5b89\u88c5\u597dGbrowse\u540e\uff0c\u987b\u77e5\u9053\u51e0\u4e2a\u4e3b\u8981\u7684\u6587\u4ef6\u5b58\u653e\u4f4d\u7f6e\uff0c\u9ed8\u8ba4\u5982\u4e0b\uff1a<\/p>\n
GBrowse-2.54\/   \u89e3\u538b\u7684GBrowse\u5b89\u88c5\u76ee\u5f55\uff0c\u5176\u4e2dbin\u76ee\u5f55\u4e0b\u6709\u5f88\u591a\u91cd\u8981\u7684\u7a0b\u5e8f\uff0c\u6bd4\u5982\u521b\u5efaGbrowse2\u7684\u7528\u6237\u7684\u7a0b\u5e8f\u7b49\u3002<\/p>\n
\/etc\/gbrowse2\/  \u5b58\u653eGbrowse\u7684\u914d\u7f6e\u6587\u4ef6\uff0c\u6709\u5168\u5c40\u7684\u914d\u7f6e\u6587\u4ef6 GBrowse.conf \u548c \u81ea\u5df1\u5efa\u7acb\u7684\u4e00\u4e2a\u7269\u79cd\u7684\u914d\u7f6e\u6587\u4ef6 species.conf;<\/p>\n
\/var\/www\/html\/gbrowse2\/  \u5b58\u653egbrowse2\u7684\u4e00\u4e9b\u7f51\u9875\u6587\u4ef6\uff0c\u6bd4\u5982gbrowse2\u7684\u4f7f\u7528\u6559\u7a0b\u7b49\uff1b<\/p>\n
\/var\/www\/cgi-bin\/gb2\/    gbrowse2\u7684web\u7a0b\u5e8f\u53ef\u6267\u884c\u6587\u4ef6\uff0c<\/p>\n
\/var\/lib\/gbrowse2\/        gbrowse2\u7684\u6570\u636e\u5e93\u76ee\u5f55\u548c\u7528\u6237\u76ee\u5f55\u7b49\u3002\u9700\u8981\u4fee\u6539\u6570\u636e\u5e93\u76ee\u5f55\u7684\u7528\u6237\u62e5\u6709\u8005\uff0c\u4ee5\u4fbf\u4e8e\u5bfc\u5165\u6570\u636e\u3002<\/p>\n
\r\n$ sudo chown chenlianfu \/var\/lib\/gbrowse2\/databases\/\r\n<\/pre>\n
2.2 \/etc\/gbrowse2\/GBrowse.conf \u51e0\u4e2a\u53ef\u80fd\u9700\u8981\u9700\u8981\u5b9a\u5236\u7684\u914d\u7f6e\uff1a<\/h2>\n
\r\n1. max_render_processes   = 12 \u8bbe\u7f6e\u6e32\u67d3\u9700\u8981\u7684\u6700\u5927CPU\u7ebf\u7a0b\u6570\r\n2. image widths        = 450 640 800 1024 1280 1440 \u8bbe\u7f6e\u57fa\u56e0\u7ec4\u6d4f\u89c8\u5668\u663e\u793a\u7684\u5bbd\u5ea6\uff0c\u53ef\u9009\u7684\u503c\uff0c\u5728perference\u9879\u4e2d\u8fdb\u884c\u8bbe\u7f6e\u65f6\u53ef\u9009\u7684\u503c\r\n   default width       = 1024  \u9ed8\u8ba4\u7684\u503c\r\n3. show sources        = 1  \u9ed8\u8ba4\u4e0b\u5f00\u542f\u4e0b\u62c9\u83dc\u5355 \u6570\u636e\u6e90 \uff0c\u4ee5\u5229\u4e8e\u8f6c\u79fb\u5230\u5176\u5b83\u7269\u79cd\u7684\u57fa\u56e0\u7ec4\u6d4f\u89c8\u4e2d\u3002\r\n4. #include \"themes\/warm_colors\"  \u57fa\u56e0\u7ec4\u6d4f\u89c8\u5668\u76843\u4e2a\u4e3b\u9898\uff0c\u6b64\u4e3a\u9ed8\u8ba4\u7684\u4e3b\u9898\u3002\r\n   # #include \"themes\/transparent_colors\"\r\n   # #include \"themes\/solid_gray_colors\"\r\n5. default source = yeast  \u8bbe\u7f6e\u57fa\u56e0\u7ec4\u6d4f\u89c8\u5668\u4e2d\u9ed8\u8ba4\u7684\u7269\u79cd\uff0c\u5373http:\/\/host\/cgi-bin\/gb2\/gbrowse\/\u9ed8\u8ba4\u6240\u8bbf\u95ee\u7684\u7269\u79cd\u3002\r\n6. [lentinula_edodes]      \u8bbe\u7f6e\u6240\u8981\u5efa\u7acb\u7684\u7269\u79cd\u7684\u57fa\u56e0\u7ec4\u6d4f\u89c8\u5668\u7684\u914d\u7f6e\u6587\u4ef6\u8def\u5f84\r\n   description = Lentinula edodes Genome\r\n   path        = lentinula_edodes.conf\r\n7. \u5728GBrowse.conf\u540c\u76ee\u5f55\u4e0b\u6709\u4e2alanguages\u7684\u6587\u4ef6\u5939\uff0c\u5176\u4e2dgbrowse2\u9ed8\u8ba4\u4f7f\u7528zh.pm\u6a21\u5757\uff0c\u4e8e\u662fGBrowse\u7684\u663e\u793a\u6587\u5b57\u9ed8\u8ba4\u662f\u7e41\u4f53\u4e2d\u6587\uff0c\u53ef\u4ee5\u4f7f\u7528\u5176\u76ee\u5f55\u4e0b\u7684\u5176\u5b83\u8bed\u8a00\u6a21\u5757\u4ee3\u66ff\u3002\r\n<\/pre>\n
2.3 Data Source Sections\u7684\u914d\u7f6e<\/h2>\n
\u5bf9\u6240\u9700\u8981\u6d4f\u89c8\u57fa\u56e0\u7ec4\u7684\u7269\u79cd\uff0c\u5219\u9700\u8981\u5efa\u7acb\u4e00\u4e2a\u4e13\u95e8\u7684\u914d\u7f6e\u6587\u4ef6\uff0c\u6bd4\u5982\u672c\u6587\u4e2d\u7684 \/etc\/gbrowse2\/lentinula_edodes.conf \u6587\u4ef6\u3002<\/p>\n
\r\n[GENERAL]                                             \u5168\u5c40\u8bbe\u7f6e\r\nrestrict      = require user chenlianfu hzaumycology  \u8bbe\u7f6e\u8be5\u57fa\u56e0\u7ec4\u6d4f\u89c8\u5668\u7684\u8bbf\u95ee\u6743\u9650\uff0c\u53ea\u6709chenlianfu\u548chzaumycology\u80fd\u8bbf\u95ee\u3002\u4f7f\u7528\u547d\u4ee4gbrowse_create_account.pl\u6765\u521b\u5efagbrowse\u7528\u6237\r\ndescription   = Lentinula edodes Genome Database      \u5bf9\u6570\u636e\u5e93\u7684\u63cf\u8ff0\r\ndatabase      = gene_Prediction_EVM                   \u6570\u636e\u5e93\u7684\u540d\u5b57\uff0c\u8fd9\u4e2a\u4e00\u5b9a\u8981\u6709\uff0c\u4e0d\u7136\u4f1a\u63d0\u793a\u9519\u8bef\u3002\u5f53\u7136\u5982\u679c\u5c06\u53ea\u6709\u4e00\u4e2a\u6570\u636e\u5e93\uff0c\u5e76\u653e\u5165\u5230GENERAL\u4e2d\uff0c\u5219\u4e0d\u9700\u8981\u8be5\u9879\r\ninitial landmark = scaffold_1:20000..40000            \u521d\u59cb\u8bbf\u95ee\u6570\u636e\u5e93\u65f6\u5019\u663e\u793a\u7684\u533a\u57df\r\ndefault tracks   = Genes_EVM                          \u521d\u59cb\u8bbf\u95ee\u6570\u636e\u5e93\u65f6\u5019\u663e\u793a\u7684tracks\r\n                   Genes_Augustus\r\nmetadata      =                                       \u5bf9\u6570\u636e\u5e93\u7684\u4e00\u4e9b\u63cf\u8ff0\r\n        -description    Lentinula edodes Genome (strain: W1-26)\r\n        -maintainer     Lianfu Chen \r\n        -created        2013-05-28\r\n        -modified       2013-05-28\r\n        -authority      hzaumycology\r\n        -coordinates    http:\/\/www.hzaumycology.com\/\r\n        -coordinates_version    1\r\n        -source         Scaffold\r\n        -testrange      scaffold_1:103361..105454\r\n        -species        Lentinula edodes W1-26\r\nexample       = scaffold_1                           \u7ed9\u51fa\u7684\u51e0\u4e2a\u4f8b\u5b50\u7528\u4e8e\u9009\u62e9\r\n                scaffold_1000:2164..4463              \r\n#################################\r\n# database definitions                               \u6570\u636e\u5e93\u8bbe\u7f6e\u3002\r\n#################################\r\n[gene_Prediction_EVM:database]                       \u7b2c\u4e00\u4e2a\u6570\u636e\u5e93\u3002\u8be5\u6570\u636e\u5e93\u7a0d\u5fae\u7279\u6b8a\u4e9b\uff0c\u5728\u5168\u5c40\u4e2d\u4f7f\u7528\u8be5\u6570\u636e\u5e93\uff0c\u9700\u8981\u5c06fasta\u6587\u4ef6\u548cscaffold\u4fe1\u606f\u5bfc\u5165\u5230\u8be5\u6570\u636e\u5e93\u3002\r\ndb_adaptor    = Bio::DB::SeqFeature::Store           \u6570\u636e\u5e93\u7684\u8bfb\u53d6\u65b9\u6cd5\r\ndb_args       = -adaptor DBI::mysql                  \u4f7f\u7528mysql\u6570\u636e\u5e93\r\n                -dsn lentinula_edodes_EVM            mysql\u6570\u636e\u5e93\u4e2d\u7684\u6570\u636e\u5e93\u540d\r\n                -user chenlianfu                     mysql\u6570\u636e\u5e93\u7684\u53ef\u5199\u7528\u6237\r\n                -password 1234567                    \u7528\u6237\u7684\u5bc6\u7801\r\nsearch options = default                             \u8be5\u6570\u636e\u5e93\u4e2d\u7684\u641c\u7d22\u9009\u9879\r\n\r\n[gene_Prediction_Augustus:database]                  \u53e6\u5916\u7684\u4e00\u4e2a\u6570\u636e\u5e93\u3002\u5c06\u4e0d\u540c\u7684\u57fa\u56e0\u6ce8\u91ca\u653e\u5165\u4e0d\u540c\u7684\u6570\u636e\u5e93\uff0c\u7136\u540e\u653e\u5165\u4e0d\u540c\u7684tracks\uff0c\u6709\u5229\u4e8e\u9605\u8bfb\u548c\u4f7f\u7528\u57fa\u56e0\u7ec4\u3002\r\ndb_adaptor    = Bio::DB::SeqFeature::Store\r\ndb_args       = -adaptor DBI::mysql\r\n                -dsn lentinula_edodes_Augustus\r\n                -user chenlianfu\r\n                -password 1234567\r\nsearch options = default\r\n########################\r\n# Default glyph settings                             \u9ed8\u8ba4\u7684glyph\u8bbe\u7f6e\r\n########################\r\n[TRACK DEFAULTS]\r\nglyph         = generic           glyph\u7684\u9ed8\u8ba4\u7c7b\u578b\r\nheight        = 10                glyph\u7684\u9ad8\u5ea6\r\nr       = black\r\nfont2color    = blue\r\nlabel density = 25                \u5f53labels\u6bd4\u8be5\u6570\u76ee\u591a\u7684\u65f6\u5019\uff0c\u5219\u5173\u95edlabels\u7684\u663e\u793a\u4ee5\u8282\u7ea6\u7a7a\u95f4\r\nbump density  = 100               \u5f53features\u7684\u6570\u76ee\u591a\u4e8e\u8be5\u503c\u7684\u65f6\u5019\uff0c \u5219\u4e0d\u5728\u5782\u76f4\u65b9\u5411\u4e0a\u663e\u793afeatures\uff0c\u5b83\u4eec\u90fd\u88ab\u9650\u5236\u5728\u4e86\u4e00\u4e2a\u6c34\u5e73\u7ebf\u4e0a\u3002\r\nlink          = AUTO              \u70b9\u51fbfeature\u7684\u65f6\u5019\uff0c\u94fe\u63a5\u5230feature\u7684\u4fe1\u606f\u6587\u6863\u4e2d\u3002\r\n################## TRACK CONFIGURATION ####################\r\n# the remainder of the sections configure individual tracks   \u8bbe\u7f6etrack\r\n###########################################################\r\n#[Genes_EVM:overview]                                      \u5c06\u8be5track\u7f6e\u4e8eoverview\u4e2d\uff0c\u800c\u4e0d\u662fdetail\u4e2d\uff0c\u6b64\u65f6\uff0c\u5206\u7c7b\u81ea\u52a8\u6210\u4e3aoverview\u3002\u597d\u5904\u662f\u5728\u6574\u4f53\u4e0a\u770b\u5230\u8be5track\u7684\u7279\u5f81\uff0c\u4f46\u662f\u7ec6\u8282\u4e0a\u5c31\u6ca1\u6cd5\u653e\u5927\u4e86\u3002\r\n#[Genes_EVM:region]                                        \u540c\u4e0a\u3002\r\n[Genes_EVM]                                                track\u540d\r\ndatabase           = gene_Prediction_EVM                   track\u6240\u7528\u5230\u7684\u6570\u636e\u5e93\r\nfeature            = gene                                  track\u6240\u7528\u7684feature\r\nglyph              = gene                                  track\u7684glyph\r\nstarnd_arrow       = 1                                     glyph\u5177\u6709\u65b9\u5411\u6027\uff1b\u6709\u4e9bglyph\u5185\u5728\u5c31\u5177\u6709\u6216\u4e0d\u5177\u65b9\u5411\u6027\uff0c\u8bbe\u7f6e\u8be5\u503c\u5219\u4e0d\u5f71\u54cd\u3002\r\nbgcolor            = peachpuff                             \u989c\u8272\r\ndecorate_introns   = 1                                     intron\u663e\u793a\u65b9\u6cd5\r\nlabel_transcripts  = 1\r\ndraw_translation   = 1\r\ncategory           = Genes                                 track\u6240\u5c5e\u7684\u5206\u7c7b\uff0c\u5bf9\u5e94\u7740gbrowse2\u7684\u201cSelect Tracks\"\u7684\u5206\u7c7b\r\nlabel_transcripts  = 1\r\nvisible            = 1                                     \u521d\u59cb\u8bbf\u95ee\u6570\u636e\u5e93\u65f6\u5019\u663e\u793a\u8be5tracks\r\nkey                = Genes Predictions Intergrated by EVM  track\u5728\u6d4f\u89c8\u5668\u4e2d\u7684\u540d\u79f0\r\ncitation           = EVM was used to integrate the genes prediction results of Augustus, SNAP and GeneMarkES ;PASA was used to add UTR annotations and Alternatively spliced isoforms.  \u8be5track\u7684\u4ecb\u7ecd\u3002\r\n\r\n[Genes_Augustus]\r\ndatabase           = gene_Prediction_Augustus\r\n#feature            = gene:AUGUSTUS                         feature\u4e3agff3\u6587\u4ef6\u7684type\uff1asource\u3002\u8fd9\u6837\u505a\u7684\u8bdd\uff0c\u5c31\u53ef\u4ee5\u4e0d\u5fc5\u5efa\u591a\u4e2amysql\u6570\u636e\u5e93\uff0c\u53ea\u9700\u8981\u628asource\u8bbe\u7f6e\u597d\u5373\u53ef\u3002\r\nfeature            = gene\r\nglyph              = gene\r\nbgcolor            = peachpuff\r\ndecorate_introns   = 1\r\nlabel_transcripts  = 1\r\ndraw_translation   = 1\r\ncategory           = Genes\r\nlabel_transcripts  = 1\r\nkey                = Genes Predicted by Augustus\r\n<\/pre>\n
3. Gbrowse\u7684\u6570\u636e\u7684\u5bfc\u5165<\/h1>\n
3.1 EVM\u5c06\u591a\u4e2a\u57fa\u56e0\u7ec4\u9884\u6d4b\u7ed3\u679c\u8fdb\u884c\u878d\u5408\u540e\uff0c\u4f7f\u7528PASA\u52a0\u4e0a5’\u548c3’\u7aef\u975e\u7ffb\u8bd1\u533a\u540e\uff0c\u5f97\u5230\u6700\u7ec8\u57fa\u56e0\u7ec4\u6ce8\u91ca\u7ed3\u679c\u3002\u5c06\u8be5\u6587\u4ef6\u5bfc\u5165\u5230mysql\u6570\u636e\u5e93 gene_Prediction_EVM \u4e2d\u3002\u7531\u4e8e\u8be5\u6700\u7ec8\u7684\u6ce8\u91ca\u7ed3\u679c\u6587\u4ef6\u4e2dmRNA\u7684Nama\u7684\u503c\u5305\u542b\u7684\u5b57\u7b26\u8fc7\u957f\uff0c\u9700\u8981\u8fdb\u884c\u7f29\u77ed\uff0c\u4ee5\u5229\u4e8e\u9605\u8bfb\uff1b\u8be5\u6587\u4ef6\u4e2d\u7684genes\u4e5f\u9700\u8981\u8fdb\u884c\u6392\u5e8f\u3002\u56e0\u6b64\u7f16\u5199\u7a0b\u5e8f\u63d0\u53d6\u51fa\u9002\u5408\u4e8egbrowse\u5bfc\u5165\u7684gff3\u6587\u4ef6\u3002\u53ef\u7528\u4e8e\u5bfc\u5165\u5230gbrowse2\u7684gff3\u6587\u4ef6\u6709\u4e00\u4e9b\u7279\u70b9\uff1a<\/p>\n
\u9996\u5148\uff0c\u6bcf\u4e2ascaffold\u3001chromosome\u6216contig\u4e4b\u524d\u8981\u6709\u4e00\u884c\u6307\u5b9a\u5176feature\u548cname\u3002\u6bd4\u5982\uff1a
\nscaffold_1      .       scaffold        1       322871  .       .       .       Name=scaffold_1
\n\u8fd9\u6837gbrowse\u624d\u80fd\u8bc6\u522bscaffod_1\u662f\u5c5e\u4e8escaffold\u7c7b\u578b\uff0c\u5e76\u6709\u4e2aName\u662fscaffold_1\u3002\u624d\u4f1a\u5c06\u5176\u5728\u57fa\u56e0\u7ec4\u6d4f\u89c8\u5668\u4e2d\u663e\u73b0\u51fa\u6765\u3002\u800c\u6b63\u5e38\u7684gff3\u6587\u4ef6\u662f\u6ca1\u6709\u8fd9\u6837\u4e00\u884c\u7684\u3002<\/p>\n
gff3\u6587\u4ef6\u4e2dmRNA\u4e2d\u7684Name\u6709\u4e9b\u592a\u957f\uff0c\u5728\u57fa\u56e0\u7ec4\u6d4f\u89c8\u5668\u4e2d\u7684\u56fe\u7247\u4e2d\u5360\u7a7a\u95f4\u592a\u5927\uff0c\u9700\u8981\u91cd\u547d\u540d\u5f97\u7b80\u6d01\u4e9b\uff1bgff3\u6587\u4ef6\u4e2dintron\u7684\u53ef\u4ee5\u53bb\u6389\uff1bgff3\u6587\u4ef6\u4e2d\u5c06feature\u4e3atranscript\u7684\u6539\u53d8\u4e3amRNA;\u53bb\u6389\u6ce8\u91ca\u884c\u7b49\u3002\u4ee5\u4e0a\u8fd9\u4e9b\u90fd\u4f1a\u5f71\u54cdgborows\u7684\u663e\u793a\u7ed3\u679c\u3002<\/p>\n
\u4f7f\u7528\u5982\u4e0b\u547d\u4ee4\u6765\u5c06\u57fa\u56e0\u9884\u6d4b\u4fe1\u606f\u5bfc\u5165\u5230\u6570\u636e\u5e93\u4e2d\uff1a<\/p>\n
\r\n$ perl parse_evm_pasa_gff3.pl LEdodesGGTrinity.gene_structures_post_PASA_updates.26576.gff3 genome.fasta        \u8be5perl\u7a0b\u5e8f\u751f\u6210\u9002\u5408\u4e8e\u5bfc\u5165gbrowse2\u7684gff3\u6587\u4ef6gbrowse.gff3 \u548c protein.fasta\u6587\u4ef6.\u540e\u8005\u4e3a\u9884\u6d4b\u7684\u86cb\u767d\u7ec4\u6587\u4ef6\u3002\r\n$ mysql -h localhost -u root -p\r\nmysql > CREATE DATABASE gene_Prediction_EVM;     \u521b\u5efa\u4e00\u4e2a\u540d\u4e3a gene_Prediction_EVM \u7684 mysql\u6570\u636e\u5e93\r\nEOF\r\nmysql > Bye\r\n$ \/usr\/local\/bin\/bp_seqfeature_load.pl -c -a DBI::mysql -d gene_Prediction_EVM -u root -p password genome.fasta gbrowse.gff3  \r\n\u8be5\u7a0b\u5e8f\u80fd\u5c06gff3\u6587\u4ef6\u6216fasta\u6587\u4ef6\u5bfc\u5165\u5230\u6570\u636e\u5e93\u3002\u5176\u53c2\u6570\uff1a\r\n-c \u6e05\u7a7a\u6570\u636e\u5e93\r\n-a \u5bfc\u5165\u7684\u6570\u636e\u5e93\u7c7b\u578b\r\n-d mysql\u6570\u636e\u5e93\u5bf9\u5e94\u7684\u6570\u636e\u5e93\u540d\u79f0\r\n-u mysql\u6570\u636e\u5e93\u7528\u6237\u540d\r\n-p mysql\u6570\u636e\u5e93\u5bc6\u7801\r\n\u8be5\u7a0b\u5e8f\u5bfc\u5165\u7684\u65f6\u95f4\u6709\u70b9\u957f\uff0c\u4f9d\u636efeature\u7684\u6570\u76ee\uff0c\u65f6\u95f4\u957f\u77ed\u4e0d\u4e00\u3002\u5bf9\u4e8e1.2\u4e07\u4e2a\u57fa\u56e0\u7684\u6ce8\u91ca\uff0c\u9700\u8981\u7ea610\u5206\u949f\u5bfc\u5165\u5b8c\u6210\u3002\r\n<\/pre>\n
3.2 \u5c06Augustus\u7684\u57fa\u56e0\u9884\u6d4b\u4fe1\u606f\u5bfc\u5165<\/p>\n
\r\nperl prepare_Augustus_gff3_for_gbrowse2.pl Agustus.gff3 > gbrowse2.gff3\r\n$ mysql -h localhost -u root -p\r\nmysql > CREATE DATABASE gene_Prediction_Augustus;     \u521b\u5efa\u4e00\u4e2a\u540d\u4e3a gene_Prediction_Augustus \u7684 mysql\u6570\u636e\u5e93\r\nEOF\r\nmysql > Bye\r\n$ \/usr\/local\/bin\/bp_seqfeature_load.pl -c -a DBI::mysql -d gene_Prediction_Augustus-u root -p password genome.fasta gbrowse2.gff3\r\n<\/pre>\n
3.3 \u5176\u5b83SNAP\u548cPASA\u7684\u57fa\u56e0\u9884\u6d4b\u4fe1\u606f\u5bfc\u5165\u548c\u4e0a\u97622\u4e2d\u4e00\u81f4\u3002\u4e0d\u8d58\u8ff0\u3002<\/p>\n
4. NGS\u6570\u636e\u7684\u5bfc\u5165<\/a><\/h1>\n
4.1 \u5b89\u88c5Bio::DB::Sam<\/a>\u3002\u9700\u8981\u6709samtools\u5b89\u88c5\uff0c\u5e76\u4e14\u8be5samtools\u7684\u5b89\u88c5\u548c\u6b63\u5e38\u5b89\u88c5\u4e0d\u4e00\u6837\u3002<\/p>\n
\r\n$ wget http:\/\/garr.dl.sourceforge.net\/project\/samtools\/samtools\/0.1.19\/samtools-0.1.19.tar.bz2\r\n$ tar jxf samtools-0.1.19.tar.bz2\r\n$ cd samtools-0.1.19\r\n$ perl -p -i -e 's\/CFLAGS.*\/CFLAGS=     -g -Wall -O2 -fPIC #-m64 #-arch ppc\/' Makefile\r\n$ make -j 8\r\n$ make clean        \u5982\u679c\u4e4b\u524d\u5df2\u7ecf\u5b89\u88c5\u8fc7samtools\u7684\u8bdd\uff0c\u9700\u8981\u4fee\u6539makefile\uff0c\u518d\u91cd\u65b0\u5b89\u88c5\r\n$ make install\r\n\r\n$ wget http:\/\/search.cpan.org\/CPAN\/authors\/id\/L\/LD\/LDS\/Bio-SamTools-1.38.tar.gz\r\n$ tar zxf Bio-SamTools-1.38.tar.gz\r\n$ cd Bio-SamTools-1.38\r\n$ perl Build.pl\r\n$ .\/Build\r\n$ sudo .\/Build install\r\n<\/pre>\n
4.2 \u4fee\u6539data source\u914d\u7f6e\u6587\u4ef6<\/p>\n
\r\n[NGS_Genome:database]\r\ndb_adaptor     = Bio::DB::Sam        # \u6570\u636e\u5e93\u7684\u8bfb\u53d6\u65b9\u6cd5                                       \r\ndb_args        = -fasta genome.fasta # \u57fa\u56e0\u7ec4\u7684fasta\u6587\u4ef6\r\n                 -bam bowtie2.bam    # NGS reads\u7684\u6bd4\u5bf9\u7ed3\u679c\r\nsearch options = default\r\n\r\n[GenomeReadCoverageXyplot]\r\nfeature        = coverage            # \u57fa\u56e0\u7ec4\u6d4b\u5e8f\u7684reads\u7684coverage\r\nglyph          = wiggle_xyplot       # \u4f7f\u7528\u5cf0\u56fe\u6765\u663e\u793areads\u7684\u8986\u76d6\u5ea6\r\ndatabase       = NGS_Genome\r\nheight         = 50\r\nfgcolor        = black\r\nbicolor_pivot  = 20                  # \u8bbe\u5b9a\u4e00\u4e2a\u989c\u8272\u53d8\u6362\u7684coverage\u503c\r\npos_color      = blue                # \u5f53coverage > \u4ee5\u4e0a\u8bbe\u7f6e\u7684\u6570\u503c\uff0cs\u4f7f\u7528\u84dd\u8272\r\nneg_color      = red                 # \u5f53coverage < \u4ee5\u4e0a\u8bbe\u7f6e\u7684\u8be5\u6570\u503c\uff0cs\u4f7f\u7528\u7ea2\u8272\r\ncategory       = GenomeReads\r\nlabel          = 0                   # labels on wiggle tracks are redundant\r\nkey            = Coverage (xyplot) of Genome NGS data\r\n\r\n[GenomeReadCoverageDensity]\r\nfeature        = coverage\r\nglyph          = wiggle_density      # \u4f7f\u7528\u5bc6\u5ea6\u6765\u663e\u793areads\u7684\u8986\u76d6\u5ea6\uff0c\u8986\u76d6\u5ea6\u8d8a\u9ad8\u5219\u7ebf\u6761\u989c\u8272\u8d8a\u6df1\r\ndatabase       = NGS_Genome\r\nheight         = 30\r\nbgcolor        = blue\r\nbicolor_pivot  = 5                   # \u5c0f\u4e8e\u8be5\u503c\uff0c\u5219\u7ebf\u6761\u65e0\u989c\u8272\r\npos_color      = blue\r\nneg_color      = red\r\ncategory       = GenomeReads\r\nlabel          = 0\r\nkey            = Coverage (density plot) of Genome NGS data\r\n\r\n[GenomeReads]                       # reads\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u7684\u56fe\u5f62\u663e\u793a\r\nfeature        = match\r\nglyph          = segments\r\ndraw_target    = 1\r\nshow_mismatch  = 1\r\nmismatch_color = red\r\ndatabase       = NGS_Genome\r\nbgcolor        = blue\r\nfgcolor        = white\r\nheight         = 5\r\nlabel density  = 50\r\nbump           = fast\r\ncategory       = GenomeReads\r\nkey            = Reads of Genome NGS data\r\n\r\n[GenomeReadsPair]                  # reads pair\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u7684\u56fe\u5f62\u663e\u793a\r\nfeature       = read_pair\r\nglyph         = segments\r\ndatabase      = NGS_Genome\r\ndraw_target   = 1\r\nshow_mismatch = 1\r\nbgcolor       = sub {\r\n                my $f = shift;\r\n                return $f->attributes('M_UNMAPPED') ? 'red' : 'green';\r\n                }\r\nfgcolor       = green\r\nheight        = 3\r\nlabel         = sub {shift->display_name}\r\nlabel density = 50\r\nbump          = fast\r\nconnector     = dashed\r\nballoon hover = sub {\r\n                my $f     = shift;\r\n                return '' unless $f->type eq 'match';\r\n                return 'Read: '.$f->display_name.' : '.$f->flag_str;\r\n                }\r\ncategory      = GenomeReads\r\nkey           = Read Pairs of Genome NGS data\r\n\r\n[GenomeReadsMappingQuality]        # reas\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u7684Mapping\u8d28\u91cf\u56fe\uff0c\u9ad8\u8d28\u91cf\u4f7f\u7528\u6df1\u84dd\u8272\u8868\u793a\uff0c\u4f4e\u8d28\u91cf\u4f7f\u7528\u6d45\u84dd\u8272\u663e\u793a\r\nfeature        = match\r\nglyph          = segments\r\ndraw_target    = 1\r\nshow_mismatch  = 1\r\nmismatch_color = red\r\ndatabase       = NGS_Genome\r\nbgcolor        = sub {\r\n        my $feature = shift;\r\n        my $blueness = 255 - int($feature->qual * 2.40);\r\n        my $colour = chr(35) . sprintf(\"%X\", $blueness) .\r\n                               sprintf(\"%X\", $blueness) . \"FF\";\r\n        return $colour;\r\n        }\r\nfgcolor        = black\r\nheight         = 5\r\nlabel density  = 50\r\nbump           = fast\r\ncategory       = GenomeReads\r\nkey            = Reads' Mapping Quality of Genome NGS data\r\n<\/pre>\n
4.3 \u5c06Bam\u6587\u4ef6\u653e\u7f6e\u5230\u914d\u7f6e\u6587\u4ef6\u4e2d\u5bf9\u5e94\u7684\u4f4d\u7f6e\u3002<\/p>\n
\u82e5\u5728track\u4e2d\u63d0\u793a\u8be5\u9519\u8bef\uff1a
\nTrack rending error: No index file for bam file; try opeing file with -autoindex at \/usr\/local\/lib64\/perl5\/Bio\/DB\/Sam.pm line 2064
\n\u5219\u8868\u793a\u7f3a\u5c11bam\u6587\u4ef6\u5bf9\u5e94\u7684index\u6587\u4ef6\u3002\u8be5\u6587\u4ef6\u4ee5bai\u4e3a\u540e\u7f00\uff0c\u4f7f\u7528samtools\u751f\u6210<\/p>\n
\r\n$ samtools index geonme.bam\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"
1. GBrowse\u7684\u5b89\u88c5 GBrowse\u5b89\u88c5\u8bf4\u660e\u6587\u6863\uff1ahttp:\/\/gmod. … \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":[1],"tags":[],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1325"}],"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=1325"}],"version-history":[{"count":28,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1325\/revisions"}],"predecessor-version":[{"id":1992,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1325\/revisions\/1992"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1325"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1325"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1325"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}