{"id":30015,"date":"2024-02-27T18:02:28","date_gmt":"2024-02-27T10:02:28","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30015"},"modified":"2024-02-27T18:02:29","modified_gmt":"2024-02-27T10:02:29","slug":"%e7%94%9f%e4%bf%a1%e4%ba%ba%e5%bf%85%e5%ad%a6%e7%9a%84%e8%bd%af%e4%bb%b6%e4%b9%8bbedtools-annotate","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=30015","title":{"rendered":"\u751f\u4fe1\u4eba\u5fc5\u5b66\u7684\u8f6f\u4ef6\u4e4bbedtools annotate"},"content":{"rendered":"<p>\u751f\u4fe1\u4eba\u5fc5\u5b66\u7684\u8f6f\u4ef6\u4e4bbedtools annotate<\/p>\n<p>Bedtools\u662f\u7531\u72b9\u4ed6\u5927\u5b66\u6606\u5170\u5b9e\u9a8c\u5ba4\u5f00\u53d1\u7684\u4e00\u4e2a\u5927\u91cf\u751f\u7269\u4fe1\u606f\u5b66\u6570\u636e\u5904\u7406\u811a\u672c\u7684\u96c6\u5408\uff0c\u5b83\u7b80\u76f4\u662f\u57fa\u56e0\u7ec4\u6570\u636e\u5206\u6790\u7684\u745e\u58eb\u519b\u5200\uff0c\u53ef\u4ee5\u5bf9bam\u3001bed\u3001GFF\/GTF\u3001VCF\u7b49\u6570\u636e\u8fdb\u884c\u5904\u7406\uff0c\u5feb\u901f\u5b8c\u6210\u53d6\u4ea4\u96c6\u3001\u5e76\u96c6\u3001\u8865\u96c6\u3001\u8ba1\u6570\u4ee5\u53ca\u683c\u5f0f\u8f6c\u6362\u7b49\u64cd\u4f5c\u3002\u90a3\u4e48\u63a5\u4e0b\u6765\uff0c\u5c0f\u679c\u5c06\u5206\u7ae0\u8282\u4e3a\u5927\u5bb6\u4ecb\u7ecdBedtools\u7684\u7528\u6cd5\u3002<\/p>\n<p>\u4eca\u5929\u8ddf\u7740\u5c0f\u679c\u6765\u5b66\u4e60annotate\u8fd9\u4e2a\u547d\u4ee4\u7684\u4f7f\u7528\u65b9\u6cd5\u5427\u3002<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"156\" class=\"wp-image-30016\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-93.png?resize=640%2C156\" alt=\"\u6587\u672c\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-93.png?w=1072 1072w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-93.png?resize=300%2C73 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-93.png?resize=1024%2C249 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-93.png?resize=768%2C187 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/unnamed-file-93.png?resize=600%2C146 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>Bedtools annotate\u547d\u4ee4\u53ef\u4ee5\u7528\u4e8e\u7edf\u8ba1\u4e00\u4e2abed\u3001vcf\u3001gff\u4e0e\u591a\u4e2abed\u3001vcf\u3001gff\u6587\u4ef6\u7684\u91cd\u53e0\u533a\u57df\u7684\u6bd4\u4f8b\u548c\u6570\u91cf\uff0c\u8fd9\u6837\u5c31\u53ef\u4ee5\u5bf9\u6bd4\u591a\u4e2a\u5e8f\u5217\u4e4b\u95f4\u7684\u76f8\u4f3c\u7a0b\u5ea6\u3002<\/p>\n<p>\u793a\u4f8b\u5982\u4e0b<\/p>\n<p>bedtools annotate [OPTIONS] -I &lt;BED\/GFF\/VCF&gt; -files FILE1 FILE2 FILE3 \u2026. FILEn<\/p>\n<p>$ cat variants.bed<\/p>\n<p>chr1 100 200 nasty 1 \u2013<\/p>\n<p>chr2 500 1000 ugly 2 +<\/p>\n<p>chr3 1000 5000 big 3 +<\/p>\n<p>$ cat genes.bed<\/p>\n<p>chr1 150 200 geneA 1 +<\/p>\n<p>chr1 175 250 geneB 2 +<\/p>\n<p>chr3 0 10000 geneC 3 &#8211;<\/p>\n<p>$ cat conserve.bed<\/p>\n<p>chr1 0 10000 cons1 1 +<\/p>\n<p>chr2 700 10000 cons2 2 \u2013<\/p>\n<p>chr3 4000 10000 cons3 3 +<\/p>\n<p>$ cat known_var.bed<\/p>\n<p>chr1 0 120 known1 \u2013<\/p>\n<p>chr1 150 160 known2 \u2013<\/p>\n<p>chr2 0 10000 know3 +<\/p>\n<p>$ bedtools annotate -I variants.bed -files genes.bed conserve.bed known_var.bed<\/p>\n<p>chr1 100 200 nasty 1 \u2013 0.500000 1.000000 0.300000<\/p>\n<p>chr2 500 1000 ugly 2 + 0.000000 0.600000 1.000000<\/p>\n<p>chr3 1000 5000 big 3 \u2013 1.000000 0.250000 0.000000<\/p>\n<p>annotation\u4f7f\u7528\u53c2\u6570\uff1a<\/p>\n<table>\n<tbody>\n<tr>\n<td>Option<\/td>\n<td>Description<\/td>\n<\/tr>\n<tr>\n<td>-Counts<\/td>\n<td>\u8f93\u51fa\u591a\u4e2a\u6587\u4ef6\u548c-i\u6587\u4ef6\u91cd\u53e0\u7684\u4e2a\u6570\uff0c\u9ed8\u8ba4\u8f93\u51fa\u7684\u662f\u591a\u4e2a\u6587\u4ef6\u4e0e-i\u6587\u4ef6\u91cd\u53e0\u7684\u6bd4\u4f8b\u3002<\/td>\n<\/tr>\n<tr>\n<td>-both<\/td>\n<td>\u540c\u65f6\u8f93\u51fa\u591a\u4e2a\u6587\u4ef6\u4e0e-i\u91cd\u53e0\u7684\u4e2a\u6570\u548c\u6bd4\u4f8b<\/td>\n<\/tr>\n<tr>\n<td>-s<\/td>\n<td>\u89c4\u5b9a\u4e86\u76f8\u540c\u7684\u6b63\u8d1f\u94fe\u3002\u53ea\u6709A\u548cB\u662f\u76f8\u540c\u7684\u6b63\u8d1f\u94fe\uff0c\u624d\u8003\u8651\u91cd\u53e0\u533a\u57df\uff0c\u9ed8\u8ba4\u8bbe\u7f6e\u4e0d\u8003\u8651\u6b63\u8d1f\u94fe\u4fe1\u606f<\/td>\n<\/tr>\n<tr>\n<td>-S<\/td>\n<td>\u89c4\u5b9a\u4e86\u76f8\u53cd\u7684\u6b63\u8d1f\u94fe\u3002\u53ea\u6709A\u548cB\u662f\u76f8\u53cd\u7684\u6b63\u8d1f\u94fe\uff0c\u624d\u8003\u8651\u91cd\u53e0\u533a\u57df\uff0c\u9ed8\u8ba4\u8bbe\u7f6e\u4e0d\u8003\u8651\u6b63\u8d1f\u94fe\u4fe1\u606f<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>\u597d\u5566\uff0cbedtools\u7684annotation\u5c31\u5b66\u4e60\u5230\u8fd9\u91cc\u5427\uff0c\u66f4\u591a\u751f\u4fe1\u77e5\u8bc6\u6b22\u8fce\u5173\u5c0f\u679c\u3002<\/p>\n<p><a id=\"post-30015-_Hlk132319777\"><\/a><strong>\u626b\u7801\u5173\u6ce8\u6211\u4eec<\/strong><\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"350\" height=\"243\" class=\"wp-image-30017\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/qr.png?resize=350%2C243\" alt=\"QR \u4ee3\u7801\n\n\u63cf\u8ff0\u5df2\u81ea\u52a8\u751f\u6210\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/qr.png?w=350 350w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/02\/qr.png?resize=300%2C208 300w\" sizes=\"(max-width: 350px) 100vw, 350px\" data-recalc-dims=\"1\" \/><\/p>\n<p>shengxinguoer<\/p>\n<p><strong>\u751f\u4fe1\u679c<\/strong><\/p>\n<p>\u751f\u4fe1\u786c\u6838\u77e5\u8bc6\u89e3\u7b54<\/p>\n<p>\u548c\u5c0f\u679c\u4e00\u8d77\u5b66\u751f\u4fe1<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u751f\u4fe1\u4eba\u5fc5\u5b66\u7684\u8f6f\u4ef6\u4e4bbedtools annotate Bedtools\u662f\u7531\u72b9\u4ed6\u5927\u5b66\u6606\u5170\u5b9e\u9a8c\u5ba4\u5f00\u53d1\u7684\u4e00\u4e2a\u5927\u91cf\u751f\u7269 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30015"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=30015"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30015\/revisions"}],"predecessor-version":[{"id":30018,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/30015\/revisions\/30018"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=30015"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=30015"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=30015"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}