{"id":5393,"date":"2024-08-12T00:38:19","date_gmt":"2024-08-11T16:38:19","guid":{"rendered":"https:\/\/fanyiming.life\/?p=5393"},"modified":"2025-12-21T01:04:40","modified_gmt":"2025-12-20T17:04:40","slug":"%e4%bb%8ebam%e6%96%87%e4%bb%b6%e4%b8%ad%e5%8e%bb%e9%99%a4rrna-reads","status":"publish","type":"post","link":"https:\/\/fanyiming.life\/?p=5393","title":{"rendered":"BAM\u6587\u4ef6\u53bb\u9664rRNA"},"content":{"rendered":"\n<blockquote class=\"wp-block-quote is-layout-flow wp-block-quote-is-layout-flow\">\n<p>Generated by ChatGPT4o<\/p>\n<\/blockquote>\n\n\n\n<h2 class=\"wp-block-heading\">\u80cc\u666f<\/h2>\n\n\n\n<p>\u5728RNA-seq\u6570\u636e\u5206\u6790\u4e2d\uff0crRNA reads\u901a\u5e38\u5360\u636e\u5927\u91cf\u6d4b\u5e8f\u6570\u636e\uff0c\u4f46\u5b83\u4eec\u5bf9\u4e8e\u5927\u591a\u6570\u7814\u7a76\u6ca1\u6709\u5b9e\u9645\u4ef7\u503c\u3002\u56e0\u6b64\uff0c\u53bb\u9664\u8fd9\u4e9brRNA reads\u662f\u6570\u636e\u9884\u5904\u7406\u7684\u91cd\u8981\u6b65\u9aa4\u3002\u672c\u6587\u5c06\u4ecb\u7ecd\u5982\u4f55\u901a\u8fc7UCSC Table Browser\u83b7\u53d6rRNA\u7684BED\u6587\u4ef6\uff0c\u5e76\u7ed3\u5408<code>samtools<\/code>\u4eceBAM\u6587\u4ef6\u4e2d\u53bb\u9664rRNA reads\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">BED\u6587\u4ef6\u683c\u5f0f\u7b80\u4ecb<\/h2>\n\n\n\n<p>BED\u6587\u4ef6\u662f\u4e00\u79cd\u6587\u672c\u683c\u5f0f\uff0c\u7528\u4e8e\u63cf\u8ff0\u57fa\u56e0\u7ec4\u533a\u57df\u3002\u7ecf\u5178\u7684BED\u6587\u4ef6\u5305\u542b\u516d\u5217\uff1a<\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li><strong>chrom<\/strong>\uff1a\u67d3\u8272\u4f53\u540d\u79f0\uff08\u5982<code>chr1<\/code>\u3001<code>chr2<\/code>\u3001<code>chrX<\/code>\uff09\u3002<\/li>\n\n\n\n<li><strong>chromStart<\/strong>\uff1a\u8d77\u59cb\u4f4d\u7f6e\uff080-based\uff09\u3002<\/li>\n\n\n\n<li><strong>chromEnd<\/strong>\uff1a\u7ed3\u675f\u4f4d\u7f6e\uff081-based\uff09\u3002<\/li>\n\n\n\n<li><strong>name<\/strong>\uff1a\u7279\u5f81\u540d\u79f0\u6216ID\uff08\u53ef\u9009\uff09\u3002<\/li>\n\n\n\n<li><strong>score<\/strong>\uff1a\u7279\u5f81\u7684\u5f97\u5206\uff08\u53ef\u9009\uff09\u3002<\/li>\n\n\n\n<li><strong>strand<\/strong>\uff1a\u94fe\u65b9\u5411\uff08<code>+<\/code> \u6216 <code>-<\/code>\uff09\u3002<\/li>\n<\/ol>\n\n\n\n<p>\u5bf9\u4e8erRNA\u533a\u57df\uff0c<code>repClass<\/code>\u5b57\u6bb5\u901a\u5e38\u6307\u5b9a\u4e3a<code>rRNA<\/code>\u3002<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">\u793a\u4f8bBED\u6587\u4ef6<\/h3>\n\n\n\n<pre class=\"wp-block-code\"><code>chr1    10000   10100   rRNA    900   +\nchr2    20000   20100   rRNA    800   -<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">\u4f7f\u7528UCSC Table Browser \u83b7\u53d6rRNA\u7684BED\u6587\u4ef6<\/h2>\n\n\n\n<h3 class=\"wp-block-heading\">Step-by-Step \u64cd\u4f5c\u6307\u5357<\/h3>\n\n\n\n<ol class=\"wp-block-list\">\n<li><strong>\u8bbf\u95eeUCSC Table Browser<\/strong>\uff1a \u6253\u5f00 <a href=\"https:\/\/genome.ucsc.edu\/\">UCSC Genome Browser<\/a>\u3002\u5728\u9876\u90e8\u83dc\u5355\u4e2d\u9009\u62e9\u201cTools\u201d\uff0c\u7136\u540e\u70b9\u51fb\u201cTable Browser\u201d\u3002<\/li>\n\n\n\n<li><strong>\u9009\u62e9\u57fa\u56e0\u7ec4\u548c\u6ce8\u91ca\u6570\u636e<\/strong>\uff1a<\/li>\n<\/ol>\n\n\n\n<ul class=\"wp-block-list\">\n<li><strong>Clade<\/strong>: \u9009\u62e9\u201cMammal\u201d\u3002<\/li>\n\n\n\n<li><strong>Genome<\/strong>: \u9009\u62e9\u201cHuman\u201d\u3002<\/li>\n\n\n\n<li><strong>Assembly<\/strong>: \u9009\u62e9\u201cGRCh38\u201d\u3002<\/li>\n\n\n\n<li><strong>Group<\/strong>: \u9009\u62e9\u201cRepeats\u201d\u3002<\/li>\n\n\n\n<li><strong>Track<\/strong>: \u9009\u62e9\u201crmsk\u201d\u3002<\/li>\n\n\n\n<li><strong>Table<\/strong>: \u9009\u62e9\u201crmsk\u201d\u3002<\/li>\n<\/ul>\n\n\n\n<ol class=\"wp-block-list\">\n<li><strong>\u8bbe\u5b9a\u67e5\u8be2\u533a\u57df<\/strong>\uff1a \u5728\u201cRegion\u201d\u90e8\u5206\uff0c\u9009\u62e9\u201cgenome\u201d\u4ee5\u641c\u7d22\u6574\u4e2a\u57fa\u56e0\u7ec4\uff0c\u6216\u8005\u6307\u5b9a\u7279\u5b9a\u7684\u67d3\u8272\u4f53\u6216\u533a\u57df\u3002<\/li>\n\n\n\n<li><strong>\u8bbe\u7f6e\u8fc7\u6ee4\u6761\u4ef6<\/strong>\uff1a \u70b9\u51fb\u201cfilter\u201d\u6309\u94ae\uff0c\u6253\u5f00\u8fc7\u6ee4\u5668\u8bbe\u7f6e\u754c\u9762\u3002\u5728<code>repClass<\/code>\u5b57\u6bb5\u4e2d\u8f93\u5165<code>rRNA<\/code>\uff0c\u4ee5\u8fc7\u6ee4\u51farRNA\u533a\u57df\u3002<\/li>\n\n\n\n<li><strong>\u5bfc\u51faBED\u6587\u4ef6<\/strong>\uff1a \u5728\u201coutput format\u201d\u4e2d\u9009\u62e9\u201cBED\u201d\u683c\u5f0f\u3002\u70b9\u51fb\u201cget output\u201d\u4e0b\u8f7d\u5305\u542brRNA\u533a\u57df\u7684BED\u6587\u4ef6\u3002<\/li>\n<\/ol>\n\n\n\n<h2 class=\"wp-block-heading\">\u4f7f\u7528<code>samtools<\/code>\u548c<code>bedtools<\/code>\u53bb\u9664rRNA reads<\/h2>\n\n\n\n<p>\u6709\u4e86rRNA\u7684BED\u6587\u4ef6\u540e\uff0c\u53ef\u4ee5\u4f7f\u7528\u4ee5\u4e0b\u6b65\u9aa4\u4eceBAM\u6587\u4ef6\u4e2d\u53bb\u9664rRNA reads\uff1a<\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li><strong>\u7d22\u5f15BAM\u6587\u4ef6<\/strong>\uff08\u5982\u679c\u5c1a\u672a\u7d22\u5f15\uff09\uff1a<\/li>\n<\/ol>\n\n\n\n<pre class=\"wp-block-code\"><code>samtools index input.bam<\/code><\/pre>\n\n\n\n<ol start=\"2\" class=\"wp-block-list\">\n<li><strong>\u4f7f\u7528<code>bedtools<\/code>\u53bb\u9664rRNA reads<\/strong>\uff1a<\/li>\n<\/ol>\n\n\n\n<pre class=\"wp-block-code\"><code>bedtools intersect -abam input.bam -b rrna.bed -v &gt; output_no_rrna.bam<\/code><\/pre>\n\n\n\n<p><code>input.bam<\/code> \u662f\u4f60\u7684\u539f\u59cbBAM\u6587\u4ef6\u3002<code>rrna.bed<\/code> \u662f\u5305\u542brRNA\u533a\u57df\u7684BED\u6587\u4ef6\u3002<code>output_no_rrna.bam<\/code> \u662f\u53bb\u9664rRNA reads\u540e\u7684BAM\u6587\u4ef6\u3002<\/p>\n\n\n\n<ol start=\"3\" class=\"wp-block-list\">\n<li><strong>\u7d22\u5f15\u53bb\u9664rRNA reads\u540e\u7684BAM\u6587\u4ef6<\/strong>\uff1a<\/li>\n<\/ol>\n\n\n\n<pre class=\"wp-block-code\"><code>samtools index output_no_rrna.bam<\/code><\/pre>\n\n\n\n<h2 class=\"wp-block-heading\">\u53e6\u4e00\u79cd\u53bb\u9664rRNA\u7684\u65b9\u6cd5\uff1a\u4f7f\u7528BBDuk<\/h2>\n\n\n\n<p>\u9664\u4e86\u4eceBAM\u6587\u4ef6\u4e2d\u53bb\u9664rRNA reads\uff0c\u53e6\u4e00\u79cd\u65b9\u6cd5\u662f\u76f4\u63a5\u4eceFASTQ\u6587\u4ef6\u4e2d\u53bb\u9664rRNA reads\u3002\u4f60\u53ef\u4ee5\u4f7f\u7528<code>BBDuk<\/code>\u5de5\u5177\uff0c\u901a\u8fc7\u4ee5\u4e0b\u547d\u4ee4\u5b9e\u73b0\uff1a<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">\u8fd0\u884cBBduk<\/h3>\n\n\n\n<pre class=\"wp-block-code\"><code>bbduk.sh in=&lt;input.fastq&gt; out=&lt;cleaned_output.fastq&gt; ref=ribokmers.fa k=27 hdist=1 stats=&lt;stats.txt&gt;<\/code><\/pre>\n\n\n\n<h4 class=\"wp-block-heading\">\u53c2\u6570\u8bf4\u660e\uff1a<\/h4>\n\n\n\n<ul class=\"wp-block-list\">\n<li><code>in=&lt;input.fastq&gt;<\/code>\uff1a\u8f93\u5165\u7684FASTQ\u6587\u4ef6\u8def\u5f84\u3002<\/li>\n\n\n\n<li><code>out=&lt;cleaned_output.fastq&gt;<\/code>\uff1a\u53bb\u9664rRNA\u540e\u7684\u8f93\u51faFASTQ\u6587\u4ef6\u8def\u5f84\u3002<\/li>\n\n\n\n<li><code>ref=ribokmers.fa<\/code>\uff1a\u5305\u542brRNA kmer\u7684\u53c2\u8003\u6587\u4ef6\u8def\u5f84\u3002<\/li>\n\n\n\n<li><code>k=27<\/code>\uff1akmer\u7684\u957f\u5ea6\u8bbe\u7f6e\u4e3a27\u3002<\/li>\n\n\n\n<li><code>hdist=1<\/code>\uff1a\u6700\u5927\u5141\u8bb8\u7684hamming\u8ddd\u79bb\uff0c\u8fd9\u91cc\u8bbe\u7f6e\u4e3a1\uff0c\u8868\u793a\u5141\u8bb81\u4e2a\u78b1\u57fa\u7684\u9519\u914d\u3002<\/li>\n\n\n\n<li><code>stats=&lt;stats.txt&gt;<\/code>\uff1a\u8f93\u51fa\u6bd4\u5bf9\u7edf\u8ba1\u4fe1\u606f\u7684\u6587\u4ef6\u8def\u5f84\u3002<\/li>\n<\/ul>\n\n\n\n<h3 class=\"wp-block-heading\">\u68c0\u67e5\u8f93\u51fa<\/h3>\n\n\n\n<p>\u6267\u884c\u547d\u4ee4\u540e\uff0c<code>&lt;cleaned_output.fastq&gt;<\/code> \u6587\u4ef6\u5c06\u5305\u542b\u53bb\u9664\u4e86rRNA\u5e8f\u5217\u7684\u6e05\u6d01\u6570\u636e\u3002\u4f60\u53ef\u4ee5\u67e5\u770b <code>&lt;stats.txt&gt;<\/code> \u6587\u4ef6\uff0c\u4e86\u89e3\u5177\u4f53\u8fc7\u6ee4\u6389\u4e86\u591a\u5c11\u5e8f\u5217\u3002\u8fd9\u4e2a\u6b65\u9aa4\u80fd\u591f\u6709\u6548\u5730\u53bb\u9664\u5305\u542brRNA\u768427-mers\uff0c\u4ece\u800c\u751f\u6210\u66f4\u4e3a\u5e72\u51c0\u7684\u6570\u636e\u7528\u4e8e\u540e\u7eed\u5206\u6790\u3002<\/p>\n\n\n\n<p><code>k=27<\/code> \u8868\u793a\u4f7f\u752827\u4e2a\u78b1\u57fa\u957f\u7684k-mer\u8fdb\u884c\u5339\u914d\u3002<code>ribokmers.fa<\/code> \u6307\u5b9a\u5305\u542brRNA\u5e8f\u5217\u7684k-mer\u5e93\uff0c\u7528\u4e8e\u8bc6\u522b\u5e76\u53bb\u9664rRNA reads\u3002<\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u603b\u7ed3<\/h2>\n\n\n\n<p>\u53bb\u9664rRNA reads\u662fRNA-seq\u6570\u636e\u9884\u5904\u7406\u4e2d\u7684\u91cd\u8981\u6b65\u9aa4\uff0c\u53ef\u4ee5\u901a\u8fc7\u4f7f\u7528rRNA\u7684BED\u6587\u4ef6\u548c<code>samtools<\/code>\u3001<code>bedtools<\/code>\uff0c\u6216\u8005\u901a\u8fc7<code>BBDuk<\/code>\u76f4\u63a5\u4eceFASTQ\u6587\u4ef6\u4e2d\u53bb\u9664\u3002\u8fd9\u4e9b\u65b9\u6cd5\u6709\u52a9\u4e8e\u63d0\u9ad8\u4e0b\u6e38\u5206\u6790\u7684\u51c6\u786e\u6027\u548c\u6709\u6548\u6027\u3002<\/p>\n\n\n\n<p><\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\u9644rRNA\u4ecb\u7ecd<\/h2>\n\n\n\n<p>human\u7684rRNA\u67095S, 5.8S, 18S, 28S\uff0c\u540e\u4e09\u8005\u6765\u81ea\u540c\u4e00\u4e2a\u524d\u4f53\u53eb45S rRNA\u3002<\/p>\n\n\n\n<blockquote class=\"wp-block-quote is-layout-flow wp-block-quote-is-layout-flow\">\n<p>45S ribosomal DNA (rDNA) arrays, or clusters, are present on human chromosomes 13, 14, 15, 21 and 22, designated RNR1 through RNR5, respectively. Each cluster consists of multiple 45S rDNA repeat units that vary in number among individuals and chromosomes, with total diploid copy number estimates ranging from 60 to &gt;800 repeat units in a human genome. The 45S rDNA repeat unit encodes a 45S rRNA precursor, transcribed by RNA polymerase I, which is processed to form the 18S, 5.8S and 28S rRNAs. Gene and RefSeq, in collaboration with HGNC, currently describe one 45S rDNA cluster, and one set of 45S precursor and product rRNAs, for each of the five human chromosomes to which these loci are localized.<\/p>\n\n\n\n<p><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/gene\/106631780\">NCBI<\/a><\/p>\n<\/blockquote>\n","protected":false},"excerpt":{"rendered":"<p>\u8fd9\u7bc7\u7b14\u8bb0\u8be6\u7ec6\u8bb0\u5f55\u4e86\u4eceRNA-seq\u6570\u636e\u4e2d\u53bb\u9664rRNA reads\u7684\u5b9e\u7528\u65b9\u6cd5\u3002\u4f5c\u8005\u7cfb\u7edf\u4ecb\u7ecd\u4e86\u5982\u4f55\u901a\u8fc7UCSC Table Browser\u83b7\u53d6rRNA\u7684BED\u6ce8\u91ca\u6587\u4ef6\uff0c\u5e76\u5229\u7528samtools\u548cbedtools\u5de5\u5177\u4eceBAM\u6587\u4ef6\u4e2d\u7cbe\u51c6\u8fc7\u6ee4\u6389\u8fd9\u4e9b\u975e\u76ee\u6807\u5e8f\u5217\u3002\u6b64\u5916\uff0c\u8fd8\u63d0\u4f9b\u4e86\u4f7f\u7528BBDuk\u4eceFASTQ\u6e90\u5934\u8fdb\u884c\u5904\u7406\u7684\u5907\u9009\u65b9\u6848\u3002<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[],"class_list":["post-5393","post","type-post","status-publish","format-standard","hentry","category-note"],"_links":{"self":[{"href":"https:\/\/fanyiming.life\/index.php?rest_route=\/wp\/v2\/posts\/5393","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/fanyiming.life\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/fanyiming.life\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/fanyiming.life\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/fanyiming.life\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=5393"}],"version-history":[{"count":2,"href":"https:\/\/fanyiming.life\/index.php?rest_route=\/wp\/v2\/posts\/5393\/revisions"}],"predecessor-version":[{"id":13954,"href":"https:\/\/fanyiming.life\/index.php?rest_route=\/wp\/v2\/posts\/5393\/revisions\/13954"}],"wp:attachment":[{"href":"https:\/\/fanyiming.life\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5393"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/fanyiming.life\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5393"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/fanyiming.life\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5393"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}