{"id":1248,"date":"2013-05-08T00:20:52","date_gmt":"2013-05-07T16:20:52","guid":{"rendered":"http:\/\/www.hzaumycology.com\/chenlianfu_blog\/?p=1248"},"modified":"2013-05-08T03:58:40","modified_gmt":"2013-05-07T19:58:40","slug":"augustus%e4%bd%bf%e7%94%a8%e6%8a%80%e5%b7%a7","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=1248","title":{"rendered":"Augustus\u4f7f\u7528\u6280\u5de7"},"content":{"rendered":"

1. Predict Genes ab initio<\/a><\/h1>\n

Ab initio prediction means that no other input is used than the target genome itself. Predict the genes in the range 7,000,001-7,500,000 of chr2R of D. melanogaster. Use the FASTA format file chr2R.fa<\/a>, which includes the whole chromosome 2R.<\/p>\n

\r\naugustus --species=fly --predictionStart=7000001 --predictionEnd=7500000 chr2R.fa > augustus.abinitio.gff   # takes ~1m\r\n<\/pre>\n
If you want the protein sequences you can retrieve them with<\/p>\n
\r\ngetAnnoFasta.pl augustus.abinitio.gff\r\n<\/pre>\n
2. Predic Genes Using Hints<\/a><\/h1>\n
\r\naugustus --species=fly --predictionStart=7000001 --predictionEnd=7500000 chr2R.fa \\\r\n  --extrinsicCfgFile=extrinsic.bug.cfg --hintsfile=hints.gff > augustus.hints.gff\r\n<\/pre>\n
3. Creating hints from ESTs or assembled RNAseq transcripts with BLAT<\/a><\/h1>\n
4. Creating hints from proteins with Exonerate<\/a><\/h1>\n
5. Run AUGUSTUS predictions parallel<\/a><\/h1>\n
6. RNAseq integration (raw reads)<\/h1>\n
6.1 Incorporating RNAseq data into AUGUSTUS predictions with BLAT<\/a> (including iterative mapping)<\/p>\n
6.2 Incorporating RNAseq data with GSNAP<\/a> (including iterative mapping) <\/p>\n
6.3 Incorporating RNAseq data with Bowtie\/Tophat<\/a> (including iterative mapping)<\/p>\n
6.4 Incorporating RNAseq data with Palmapper?<\/a><\/p>\n
7. Training AUGUSTUS<\/a><\/h1>\n","protected":false},"excerpt":{"rendered":"
1. Predict Genes ab initio Ab initio pre … \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\/1248"}],"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=1248"}],"version-history":[{"count":8,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1248\/revisions"}],"predecessor-version":[{"id":1259,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/1248\/revisions\/1259"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=1248"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=1248"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=1248"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}