{"id":2284,"date":"2015-08-25T16:34:47","date_gmt":"2015-08-25T08:34:47","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2284"},"modified":"2015-08-25T16:35:01","modified_gmt":"2015-08-25T08:35:01","slug":"%e4%bd%bf%e7%94%a8-hisat-%e5%b0%86%e8%bd%ac%e5%bd%95%e7%bb%84%e6%95%b0%e6%8d%ae-mapping-%e5%88%b0%e5%9f%ba%e5%9b%a0%e7%bb%84%e5%ba%8f%e5%88%97","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2284","title":{"rendered":"\u4f7f\u7528 HISAT \u5c06\u8f6c\u5f55\u7ec4\u6570\u636e mapping \u5230\u57fa\u56e0\u7ec4\u5e8f\u5217"},"content":{"rendered":"<h1>1. HISAT \u7b80\u4ecb<\/h1>\n<p><a href=\"http:\/\/www.ccb.jhu.edu\/software\/hisat\/index.shtml\" target=\"_blank\">HISAT<\/a>\uff1ahical Indexing for Spliced Alignment of Transcripts\u3002\u8be5\u8f6f\u4ef6\u548c tophat \u5f00\u53d1\u4e8e\u540c\u4e00\u4e2a\u5355\u4f4d\uff0c\u5b83\u76f8\u5f53\u4e8e tophat \u7684\u5347\u7ea7\u7248\uff0c\u6bd4\u5bf9\u901f\u5ea6\u6bd4 tophat2 \u5feb50\u500d\u3002<\/p>\n<h1>2. HISAT \u7684\u4e0b\u8f7d\u548c\u5b89\u88c5<\/h1>\n<pre>\r\n$ wget http:\/\/www.ccb.jhu.edu\/software\/hisat\/downloads\/hisat-0.1.5-beta-Linux_x86_64.zip\r\n$ unzip hisat-0.1.5-beta-Linux_x86_64.zip -d \/opt\/biosoft\/\r\n$ echo 'PATH=$PATH:\/opt\/biosoft\/hisat-0.1.5-beta\/' >> ~\/.bashrc\r\n$ source ~\/.bahsrc\r\n<\/pre>\n<h1>2. HISAT \u4f7f\u7528<\/h1>\n<h2>2.1 \u6784\u5efa\u7d22\u5f15\u6587\u4ef6<\/h12>\n<pre>\r\n$ hisat-build genome.fasta genome\r\n<\/pre>\n<h2>2.2 \u8fdb\u884c\u6bd4\u5bf9<\/h12>\n\u4ea7\u7528\u7684\u547d\u4ee4\u4e0e\u53c2\u6570\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n$ hisat -x genome -u 1000000 -p 24 -I 0 -X 500 --rna-strandness RF -1 reads.1.fastq -2 reads.2.fastq -U single.fastq -S result.sam \r\n<\/pre>\n<p>hisat \u4e0e bowtie2 \u7684\u53c2\u6570\u57fa\u672c\u4e00\u81f4\uff0c\u5e38\u7528\u7684\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-x    \u8f93\u5165\u7d22\u5f15\u6570\u636e\u5e93\r\n-1    \u8f93\u5165 reads1\r\n-2    \u8f93\u5165 reads2\r\n-U    \u8f93\u5165\u5355\u6bb5\u5e8f\u5217\r\n-u    \u4ec5\u5bf9\u524d\u591a\u5c11\u4e2areads\u8fdb\u884c\u6bd4\u5bf9\r\n-I    \u6700\u5c0f\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\r\n-X    \u6700\u5927\u63d2\u5165\u7247\u6bb5\u957f\u5ea6\r\n-S    \u8f93\u51fasam\u6587\u4ef6\r\n--rna-strandness \u94fe\u7279\u5f02\u6027\u6d4b\u5e8f\uff0c\u4e00\u822c\u4e3a RF\r\n-k    \u4e00\u4e2areads\u6bd4\u5bf9\u5230\u591a\u4e2a\u5730\u65b9\uff0c\u62a5\u544a\u51e0\u4e2a\u7ed3\u679c\uff0c\u9ed8\u8ba4\u4e3a 5 \u3002\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. HISAT \u7b80\u4ecb HISAT\uff1ahical Indexing for Spl &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2284\">\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":[70],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2284"}],"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=2284"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2284\/revisions"}],"predecessor-version":[{"id":2285,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2284\/revisions\/2285"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2284"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2284"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2284"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}