{"id":2340,"date":"2015-08-25T17:02:28","date_gmt":"2015-08-25T09:02:28","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2340"},"modified":"2015-08-25T17:02:28","modified_gmt":"2015-08-25T09:02:28","slug":"%e4%bd%bf%e7%94%a8-abyss-%e8%bf%9b%e8%a1%8c-scaffolding","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2340","title":{"rendered":"\u4f7f\u7528 abyss \u8fdb\u884c scaffolding"},"content":{"rendered":"<h1>1. ABySS \u8fdb\u884c scaffolding \u7684\u76ee\u7684\u4e0e\u4f18\u70b9<\/h1>\n<p>\u76ee\u7684\uff1a \u5bf9\u5176\u5b83\u57fa\u56e0\u7ec4 denovo \u7684 assembly \u7ed3\u679c\uff0c\u4f7f\u7528 abyss \u518d\u8fdb\u884c\u4e00\u6b21 scaffolding\u3002<br \/>\n\u4f18\u70b9\uff1a \u53ef\u4ee5\u4f7f\u7528 RNA-seq \u7684\u8f6c\u5f55\u5b50\u6570\u636e\u8fdb\u884c\u57fa\u56e0\u7ec4\u7684\u8f85\u52a9\u7ec4\u88c5\u3002<\/p>\n<h1>2. ABySS \u8fdb\u884c scaffolding \u7684\u547d\u4ee4\u884c<\/h1>\n<p>\u8f93\u5165\u6587\u4ef6\uff1a assembly.fasta, 2000.1.fastq, 2000.2.fastq, 5000.1.fastq, 5000.2.fastq\u3002<br \/>\n\u8f93\u5165\u6587\u4ef6\u662f\u57fa\u56e0\u7ec4\u7684\u7ec4\u88c5\u7ed3\u679c\uff0c\u548c 3 \u5bf9 mate-paired Illumina \u6570\u636e\u3002<\/p>\n<h2>2.1 \u5bf9 assembly.fasta \u8fdb\u884c\u5e8f\u5217\u6539\u540d<\/h2>\n<pre>\r\n\u53bb\u9664\u5e8f\u5217\u4e4b\u95f4\u7684\u6362\u884c\r\nfasta_no_blank.pl assembly.fasta > 11; mv 11 assembly.fasta\r\n\u7ed9\u5e8f\u5217\u6309\u987a\u5e8f\u91cd\u547d\u540d\r\nperl -e '$num = 0; while (<>) {if (\/^>\/) { s\/>(.*)\/>$num\/; print; $num ++; } else { print } }' assembly.fasta > ledodes-6.fa\r\n<\/pre>\n<h2>2.2 \u5c06 mate-paired \u6570\u636e\u6bd4\u5bf9\u5230\u57fa\u56e0\u7ec4\u5e8f\u5217\u4e0a<\/h2>\n<p>\u6839\u636e\u6bd4\u5bf9\u7ed3\u679c\uff0c\u5f97\u5230 mate-paired library \u7684 insertSize \u4fe1\u606f\uff08\u4ee5 .hist \u4e3a\u540e\u7f00\u7684\u6587\u4ef6\uff09\u548c \u5e8f\u5217\u4e4b\u95f4\u7684\u8fde\u63a5\u3001\u8ddd\u79bb\u4e0e\u987a\u5e8f\u4fe1\u606f (\u4ee5 .dist.dot \u4e3a\u540e\u7f00\u7684 graph \u6587\u4ef6\uff09\u3002<\/p>\n<pre>\r\nabyss-map -j24 -l87 3000.1.fastq 3000.2.fastq ledodes-6.fa \\\r\n  |abyss-fixmate -l87 -h mp1-6.hist \\\r\n  |sort -snk3 -k4 \\\r\n  |DistanceEst --dot -j24 -k87 -l87 -s200 -n10 -o mp1-6.dist.dot mp1-6.hist\r\nabyss-map -j24 -l87 8000.1.fastq 8000.2.fastq ledodes-6.fa \\\r\n  |abyss-fixmate -l87 -h mp2-6.hist \\\r\n  |sort -snk3 -k4 \\\r\n  |DistanceEst --dot -j24 -k87 -l87 -s200 -n10 -o mp2-6.dist.dot mp2-6.hist\r\n<\/pre>\n<p>\u4ee5\u4e0a\u547d\u4ee4\u884c\u4e2d\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-j24\r\n    \u4f7f\u7528 24 \u4e2a\u7ebf\u7a0b\u8fd0\u884c\r\n-l87\r\n    \u4f7f\u7528\u7684 kmer\u503c \u4e3a 87\r\n-s200\r\n    sedd contigs\u7684\u6700\u5c0f\u957f\u5ea6\u4e3a 200bp\r\n-n10\r\n    \u6240\u5141\u8bb8\u8fde\u63a5\u4e24\u6761\u5e8f\u5217\u7684\u6700\u5c0f\u7684pairs\u7684\u6570\u76ee\r\n<\/pre>\n<h2>2.3 \u8fdb\u884c scaffolding<\/h2>\n<pre>\r\nabyss-scaffold -k87 -s200 -n5 -g ledodes-6.path.dot ledodes-6.fa mp1-6.dist.dot mp2-6.dist.dot > ledodes-6.path\r\nPathConsensus -k87 -p0.9 -s ledodes-7.fa -g ledodes-7.adj -o ledodes-7.path ledodes-6.fa ledodes-6.fa ledodes-6.path\r\ncat ledodes-6.fa ledodes-7.fa \\\r\n  | MergeContigs -k87 -o ledodes-8.fa - ledodes-7.adj ledodes-7.path\r\nln -sf ledodes-8.fa ledodes-scaffolds.fa\r\nPathOverlap --overlap --dot -k87 ledodes-7.adj ledodes-7.path > ledodes-8.dot\r\n<\/pre>\n<h2>2.4 \u4f7f\u7528\u8f6c\u5f55\u5b50\u5e8f\u5217\u8fdb\u884c rescaffolding<\/h2>\n<pre>\r\nbwa index ledodes-8.fa\r\nbwa mem -a -t2 -S -P -k87 ledodes-8.fa transcripts.fasta \\\r\n  |gzip > long1-8.sam.gz\r\nabyss-longseqdist -k87 long1-8.sam.gz \\\r\n  |grep -v \"l=\" >long1-8.dist.dot\r\nabyss-scaffold -k87 -s200 -n1 -g ledodes-8.path.dot ledodes-8.dot long1-8.dist.dot > ledodes-8.path\r\nPathConsensus -k87 -p0.9 -s ledodes-9.fa -g ledodes-9.adj -o ledodes-9.path ledodes-8.fa ledodes-8.dot ledodes-8.path\r\ncat ledodes-8.fa ledodes-9.fa \\\r\n  | MergeContigs -k87 -o ledodes-10.fa - ledodes-9.adj ledodes-9.path\r\nln -sf ledodes-10.fa ledodes-long-scaffs.fa\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. ABySS \u8fdb\u884c scaffolding \u7684\u76ee\u7684\u4e0e\u4f18\u70b9 \u76ee\u7684\uff1a \u5bf9\u5176\u5b83\u57fa\u56e0 &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2340\">\u7ee7\u7eed\u9605\u8bfb <span class=\"meta-nav\">&rarr;<\/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":[39,40],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2340"}],"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=2340"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2340\/revisions"}],"predecessor-version":[{"id":2341,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2340\/revisions\/2341"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2340"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2340"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2340"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}