{"id":2438,"date":"2017-04-03T22:17:10","date_gmt":"2017-04-03T14:17:10","guid":{"rendered":"http:\/\/www.chenlianfu.com\/?p=2438"},"modified":"2017-04-03T22:17:10","modified_gmt":"2017-04-03T14:17:10","slug":"%e4%bd%bf%e7%94%a8htseq%e8%bf%9b%e8%a1%8c%e6%9c%89%e5%8f%82%e8%bd%ac%e5%bd%95%e7%bb%84%e7%9a%84%e8%a1%a8%e8%be%be%e9%87%8f%e8%ae%a1%e7%ae%97","status":"publish","type":"post","link":"http:\/\/www.chenlianfu.com\/?p=2438","title":{"rendered":"\u4f7f\u7528HTSeq\u8fdb\u884c\u6709\u53c2\u8f6c\u5f55\u7ec4\u7684\u8868\u8fbe\u91cf\u8ba1\u7b97"},"content":{"rendered":"<h1>1. HTSeq\u7b80\u4ecb<\/h1>\n<p><a href=\"http:\/\/www-huber.embl.de\/HTSeq\/doc\/overview.html\" target=\"_blank\">HTSeq<\/a>\u662f\u4f7f\u7528Python\u7f16\u5199\u7684\u4e00\u652f\u7528\u4e8e\u8fdb\u884c\u57fa\u56e0Count\u8868\u8fbe\u91cf\u5206\u6790\u7684\u8f6f\u4ef6\uff0c\u80fd\u6839\u636eSAM\/BAM\u6bd4\u5bf9\u7ed3\u679c\u6587\u4ef6\u548c\u57fa\u56e0\u7ed3\u6784\u6ce8\u91caGTF\u6587\u4ef6\u5f97\u5230\u57fa\u56e0\u6c34\u5e73\u7684Counts\u8868\u8fbe\u91cf\u3002HTSeq\u8fdb\u884cCounts\u8ba1\u7b97\u7684\u539f\u7406\u975e\u5e38\u7b80\u5355\u6613\u61c2\uff0c\u5bb9\u6613\u4e0a\u624b\u3002<\/p>\n<h1>2. HTSeq\u5b89\u88c5<\/h1>\n<pre>\r\n\u5728<a href=\"https:\/\/pypi.python.org\/pypi\" target=\"_blank\">PYPI<\/a>\u4e0b\u8f7dHTSeq\u7684Python\u5305\r\n$ wget https:\/\/pypi.python.org\/packages\/46\/f7\/6105848893b1d280692eac4f4f3c08ed7f424cec636aeda66b50bbcf217e\/HTSeq-0.7.2.tar.gz\r\n$ tar zxf HTSeq-0.7.2.tar.gz\r\n$ cd HTSeq-0.7.2\r\n$ \/opt\/sysoft\/Python-2.7.11\/bin\/python setup.py build\r\n$ \/opt\/sysoft\/Python-2.7.11\/bin\/python setup.py install\r\n$ cd ..\/ && rm HTSeq-0.7.2 -rf\r\n<\/pre>\n<h1>3. <a href=\"http:\/\/www-huber.embl.de\/HTSeq\/doc\/count.html\" target=\"_blank\">HTSeq\u4f7f\u7528<\/a><\/h1>\n<h2>3.1 HTSeq\u7684Count\u6a21\u5f0f<\/h2>\n<p>HTSeq\u8ba1\u7b97counts\u6570\u67093\u79cd\u6a21\u5f0f\uff0c\u5982\u4e0b\u56fe\u6240\u793a\uff08ambiguous\u8868\u793a\u8be5read\u6bd4\u5bf9\u5230\u591a\u4e2agene\u4e0a\uff1bno_feature\u8868\u793aread\u6ca1\u6709\u6bd4\u5bf9\u5230gene\u4e0a\uff09\uff1a<br \/>\n<img src=\"http:\/\/www-huber.embl.de\/HTSeq\/doc\/_images\/count_modes.png\" alt=\"HTSeq Count\u6a21\u5f0f\" \/><\/p>\n<h2>3.2 HTSeq\u7684\u4f7f\u7528\u547d\u4ee4<\/h2>\n<p>HTseq\u5b89\u88c5\u5b8c\u6bd5\u540e\uff0c\u5728Python\u8f6f\u4ef6\u7684bin\u76ee\u5f55\u4e0b\u751f\u6210htseq-count\u547d\u4ee4\u3002<br \/>\nhtseq-count\u8fd0\u884c\u7b80\u5355\u793a\u4f8b\uff1a<\/p>\n<pre>\r\n\u5bf9\u4e8e\u975e\u94fe\u7279\u5f02\u6027\u771f\u6838\u8f6c\u5f55\u7ec4\u6d4b\u5e8f\u6570\u636e\r\n$ \/opt\/sysoft\/Python-2.7.11\/bin\/htseq-count -f sam -r name -s no -a 10 -t exon -i gene_id -m union hisat2.sam genome.gtf > counts_out.txt\r\n\u5bf9\u4e8e\u94fe\u7279\u5f02\u6027\u6d4b\u5e8f\u771f\u6838\u8f6c\u5f55\u7ec4\u6d4b\u5e8f\u6570\u636e\r\n$ \/opt\/sysoft\/Python-2.7.11\/bin\/htseq-count -f sam -r name -s reverse -a 10 -t exon -i gene_id -m union hisat2.sam genome.gtf > counts_out.txt\r\n\u5bf9\u4e8e\u975e\u94fe\u7279\u5f02\u6027\u539f\u6838\u751f\u7269\u8f6c\u5f55\u7ec4\u6d4b\u5e8f\u6570\u636e\r\n$ \/opt\/sysoft\/Python-2.7.11\/bin\/htseq-count -f sam -r name -s no -a 10 -t exon -i gene_id -m intersection-strict bowtie2.sam genome.gtf > counts_out.txt\r\n<\/pre>\n<p>htseq-count\u547d\u4ee4\u7684\u5e38\u7528\u53c2\u6570\uff1a<\/p>\n<pre>\r\n-f | --format <string>    default: sam\r\n  \u8bbe\u7f6e\u8f93\u5165\u6587\u4ef6\u7684\u683c\u5f0f\uff0c\u8be5\u53c2\u6570\u7684\u503c\u53ef\u4ee5\u662fsam\u6216bam\u3002\r\n-r | --order <string>    default: name\r\n  \u8bbe\u7f6esam\u6216bam\u6587\u4ef6\u7684\u6392\u5e8f\u65b9\u5f0f\uff0c\u8be5\u53c2\u6570\u7684\u503c\u53ef\u4ee5\u662fname\u6216pos\u3002\u524d\u8005\u8868\u793a\u6309read\u540d\u8fdb\u884c\u6392\u5e8f\uff0c\u540e\u8005\u8868\u793a\u6309\u6bd4\u5bf9\u7684\u53c2\u8003\u57fa\u56e0\u7ec4\u4f4d\u7f6e\u8fdb\u884c\u6392\u5e8f\u3002\u82e5\u6d4b\u5e8f\u6570\u636e\u662f\u53cc\u672b\u7aef\u6d4b\u5e8f\uff0c\u5f53\u8f93\u5165sam\/bam\u6587\u4ef6\u662f\u6309pos\u65b9\u5f0f\u6392\u5e8f\u7684\u65f6\u5019\uff0c\u4e24\u7aefreads\u7684\u6bd4\u5bf9\u7ed3\u679c\u5728sam\/bam\u6587\u4ef6\u4e2d\u4e00\u822c\u4e0d\u662f\u7d27\u90bb\u7684\u4e24\u884c\uff0c\u7a0b\u5e8f\u4f1a\u5c06reads\u5bf9\u7684\u7b2c\u4e00\u4e2a\u6bd4\u5bf9\u7ed3\u679c\u653e\u5165\u5185\u5b58\uff0c\u76f4\u5230\u8bfb\u53d6\u5230\u53e6\u4e00\u7aefread\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\u56e0\u6b64\uff0c\u9009\u62e9pos\u53ef\u80fd\u4f1a\u5bfc\u81f4\u7a0b\u5e8f\u4f7f\u7528\u8f83\u591a\u7684\u5185\u5b58\uff0c\u5b83\u4e5f\u9002\u5408\u4e8e\u672a\u6392\u5e8f\u7684sam\/bam\u6587\u4ef6\u3002\u800cpos\u6392\u5e8f\u5219\u8868\u793a\u7a0b\u5e8f\u8ba4\u4e3a\u53cc\u672b\u7aef\u6d4b\u5e8f\u7684reads\u6bd4\u5bf9\u7ed3\u679c\u5728\u7d27\u90bb\u7684\u4e24\u884c\u4e0a\uff0c\u4e5f\u9002\u5408\u4e8e\u5355\u7aef\u6d4b\u5e8f\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\u5f88\u591a\u5176\u5b83\u8868\u8fbe\u91cf\u5206\u6790\u8f6f\u4ef6\u8981\u6c42\u8f93\u5165\u7684sam\/bam\u6587\u4ef6\u662f\u6309pos\u6392\u5e8f\u7684\uff0c\u4f46HTSeq\u63a8\u8350\u4f7f\u7528name\u6392\u5e8f\uff0c\u4e14\u4e00\u822c\u6bd4\u5bf9\u8f6f\u4ef6\u7684\u9ed8\u8ba4\u8f93\u51fa\u7ed3\u679c\u4e5f\u662f\u6309name\u8fdb\u884c\u6392\u5e8f\u7684\u3002\r\n-s | --stranded <yes\/no\/reverse>    default: yes\r\n  \u8bbe\u7f6e\u662f\u5426\u662f\u94fe\u7279\u5f02\u6027\u6d4b\u5e8f\u3002\u8be5\u53c2\u6570\u7684\u503c\u53ef\u4ee5\u662fyes,no\u6216reverse\u3002no\u8868\u793a\u975e\u94fe\u7279\u5f02\u6027\u6d4b\u5e8f\uff1b\u82e5\u662f\u5355\u7aef\u6d4b\u5e8f\uff0cyes\u8868\u793aread\u6bd4\u5bf9\u5230\u4e86\u57fa\u56e0\u7684\u6b63\u4e49\u94fe\u4e0a\uff1b\u82e5\u662f\u53cc\u672b\u7aef\u6d4b\u5e8f\uff0cyes\u8868\u793aread1\u6bd4\u5bf9\u5230\u4e86\u57fa\u56e0\u6b63\u4e49\u94fe\u4e0a\uff0cread2\u6bd4\u5bf9\u5230\u57fa\u56e0\u8d1f\u4e49\u94fe\u4e0a\uff1breverse\u8868\u793a\u53cc\u672b\u7aef\u6d4b\u5e8f\u60c5\u51b5\u4e0b\u4e0eyes\u503c\u76f8\u53cd\u7684\u7ed3\u679c\u3002\u6839\u636e\u8bf4\u660e\u6587\u4ef6\u7684\u7406\u89e3\uff0c\u4e00\u822c\u60c5\u51b5\u4e0b\u53cc\u672b\u7aef\u94fe\u7279\u5f02\u6027\u6d4b\u5e8f\uff0c\u8be5\u53c2\u6570\u7684\u503c\u5e94\u8be5\u9009\u62e9reverse\uff08\u672c\u4eba\u6682\u65f6\u6ca1\u6709\u6d4b\u8bd5\u8be5\u53c2\u6570\uff09\u3002\r\n-a | --a <int>    default: 10\r\n  \u5ffd\u7565\u6bd4\u5bf9\u8d28\u91cf\u4f4e\u4e8e\u6b64\u503c\u7684\u6bd4\u5bf9\u7ed3\u679c\u3002\u57280.5.4\u7248\u672c\u4ee5\u524d\u8be5\u53c2\u6570\u9ed8\u8ba4\u503c\u662f0\u3002\r\n-t | --type <string>    default: exon\r\n  \u7a0b\u5e8f\u4f1a\u5bf9\u8be5\u6307\u5b9a\u7684feature\uff08gtf\/gff\u6587\u4ef6\u7b2c\u4e09\u5217\uff09\u8fdb\u884c\u8868\u8fbe\u91cf\u8ba1\u7b97\uff0c\u800cgtf\/gff\u6587\u4ef6\u4e2d\u5176\u5b83\u7684feature\u90fd\u4f1a\u88ab\u5ffd\u7565\u3002\r\n-i | --idattr <string>    default: gene_id\r\n  \u8bbe\u7f6efeature ID\u662f\u7531gtf\/gff\u6587\u4ef6\u7b2c9\u5217\u90a3\u4e2a\u6807\u7b7e\u51b3\u5b9a\u7684\uff1b\u82e5gtf\/gff\u6587\u4ef6\u591a\u884c\u5177\u6709\u76f8\u540c\u7684feature ID\uff0c\u5219\u5b83\u4eec\u6765\u81ea\u540c\u4e00\u4e2afeature\uff0c\u7a0b\u5e8f\u4f1a\u8ba1\u7b97\u8fd9\u4e9bfeatures\u7684\u8868\u8fbe\u91cf\u4e4b\u548c\u8d4b\u7ed9\u76f8\u5e94\u7684feature ID\u3002\r\n-m | --mode <string>    default: union\r\n  \u8bbe\u7f6e\u8868\u8fbe\u91cf\u8ba1\u7b97\u6a21\u5f0f\u3002\u8be5\u53c2\u6570\u7684\u503c\u53ef\u4ee5\u6709union, intersection-strict and intersection-nonempty\u3002\u8fd9\u4e09\u79cd\u6a21\u5f0f\u7684\u9009\u62e9\u8bf7\u89c1\u4e0a\u9762\u5bf9\u8fd93\u79cd\u6a21\u5f0f\u7684\u793a\u610f\u56fe\u3002\u4ece\u56fe\u4e2d\u53ef\u77e5\uff0c\u5bf9\u4e8e\u539f\u6838\u751f\u7269\uff0c\u63a8\u8350\u4f7f\u7528intersection-strict\u6a21\u5f0f\uff1b\u5bf9\u4e8e\u771f\u6838\u751f\u7269\uff0c\u63a8\u8350\u4f7f\u7528union\u6a21\u5f0f\u3002\r\n-o | --samout <string>\r\n  \u8f93\u51fa\u4e00\u4e2asam\u6587\u4ef6\uff0c\u8be5sam\u6587\u4ef6\u7684\u6bd4\u5bf9\u7ed3\u679c\u4e2d\u591a\u4e86\u4e00\u4e2aXF\u6807\u7b7e\uff0c\u8868\u793a\u8be5read\u6bd4\u5bf9\u5230\u4e86\u67d0\u4e2afeature\u4e0a\u3002\r\n-q | --quiet\r\n  \u4e0d\u8f93\u51fa\u7a0b\u5e8f\u8fd0\u884c\u7684\u72b6\u6001\u4fe1\u606f\u548c\u8b66\u544a\u4fe1\u606f\u3002\r\n-h | --help\r\n  \u8f93\u51fa\u5e2e\u52a9\u4fe1\u606f\u3002\r\n<\/pre>\n<h2>3.3 HTSeq\u4f7f\u7528\u6ce8\u610f\u4e8b\u9879<\/h2>\n<p>HTSeq\u7684\u4f7f\u7528\u6709\u5982\u4e0b\u6ce8\u610f\u4e8b\u9879\uff0c\u5426\u5219\u5f97\u5230\u7684\u7ed3\u679c\u662f\u9519\u8bef\u7684\uff1a<\/p>\n<pre>\r\n1. HTSeq\u662f\u5bf9\u6709\u53c2\u8003\u57fa\u56e0\u7ec4\u7684\u8f6c\u5f55\u7ec4\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u8868\u8fbe\u91cf\u5206\u6790\u7684\uff0c\u5176\u8f93\u5165\u6587\u4ef6\u5fc5\u987b\u6709SAM\u548cGTF\u6587\u4ef6\u3002\r\n2. \u4e00\u822c\u60c5\u51b5\u4e0bHTSeq\u5f97\u5230\u7684Counts\u7ed3\u679c\u4f1a\u7528\u4e8e\u4e0b\u4e00\u6b65\u4e0d\u540c\u6837\u54c1\u95f4\u7684\u57fa\u56e0\u8868\u8fbe\u91cf\u5dee\u5f02\u5206\u6790\uff0c\u800c\u4e0d\u662f\u4e00\u4e2a\u6837\u54c1\u5185\u90e8\u57fa\u56e0\u7684\u8868\u8fbe\u91cf\u6bd4\u8f83\u3002\u56e0\u6b64\uff0cHTSeq\u8bbe\u7f6e\u4e86-a\u53c2\u6570\u7684\u9ed8\u8ba4\u503c10\uff0c\u6765\u5ffd\u7565\u6389\u6bd4\u5bf9\u5230\u591a\u4e2a\u4f4d\u7f6e\u7684reads\u4fe1\u606f\uff0c\u5176\u7ed3\u679c\u6709\u5229\u4e8e\u540e\u7eed\u7684\u5dee\u5f02\u5206\u6790\u3002\r\n3. \u8f93\u5165\u7684GTF\u6587\u4ef6\u4e2d\u4e0d\u80fd\u5305\u542b\u53ef\u53d8\u526a\u63a5\u4fe1\u606f\uff0c\u5426\u5219HTSeq\u4f1a\u8ba4\u4e3a\u6bcf\u4e2a\u53ef\u53d8\u526a\u63a5\u90fd\u662f\u5355\u72ec\u7684\u57fa\u56e0\uff0c\u5bfc\u81f4\u80fd\u6bd4\u5bf9\u5230\u591a\u4e2a\u53ef\u53d8\u526a\u63a5\u8f6c\u5f55\u672c\u4e0a\u7684reads\u7684\u8ba1\u7b97\u7ed3\u679c\u662fambiguous\uff0c\u4ece\u800c\u4e0d\u80fd\u8ba1\u7b97\u5230\u57fa\u56e0\u7684count\u4e2d\u3002\u5373\u4f7f\u8bbe\u7f6e-i\u53c2\u6570\u7684\u503c\u4e3atranscript_id\uff0c\u5176\u7ed3\u679c\u4e00\u6837\u662f\u4e0d\u51c6\u786e\u7684\uff0c\u53ea\u662f\u5f97\u5230transcripts\u7684\u8868\u8fbe\u91cf\u3002\r\n<\/pre>\n<h2>3.4 HTSeq\u7684\u7ed3\u679c<\/h2>\n<p>HTSeq\u5c06Count\u7ed3\u679c\u8f93\u51fa\u5230\u6807\u51c6\u8f93\u51fa\uff0c\u5176\u7ed3\u679c\u793a\u4f8b\u5982\u4e0b\uff1a<\/p>\n<pre>\r\ngene00001\t0\r\ngene00002\t9224\r\ngene00003\t880\r\n...\r\ngene12300\t1043\r\ngene12301\t200\r\n__no_feature\t127060\r\n__ambiguous\t0\r\n__too_low_aQual\t4951\r\n__not_aligned\t206135\r\n__alignment_not_unique\t0\r\n<\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. HTSeq\u7b80\u4ecb HTSeq\u662f\u4f7f\u7528Python\u7f16\u5199\u7684\u4e00\u652f\u7528\u4e8e\u8fdb\u884c\u57fa\u56e0Coun &hellip; <a href=\"http:\/\/www.chenlianfu.com\/?p=2438\">\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":[30],"_links":{"self":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2438"}],"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=2438"}],"version-history":[{"count":1,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2438\/revisions"}],"predecessor-version":[{"id":2439,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=\/wp\/v2\/posts\/2438\/revisions\/2439"}],"wp:attachment":[{"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2438"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2438"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.chenlianfu.com\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2438"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}