<\/title><br \/>\n<meta charset=\"utf-8\"><br \/>\n<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0,maximum-scale=1.0,user-scalable=0,viewport-fit=cover\"><\/p>\n<style>\n*{margin:0;padding:0}html{-ms-text-size-adjust:100%;-webkit-text-size-adjust:100%;line-height:1.6}img{z-index:999;position:relative;max-width:100%;margin:10px 0;}body{letter-spacing:.034em}h1,h2,h3,h4,h5,h6{font-weight:400;font-size:16px}a{color:#576b95;text-decoration:none;-webkit-tap-highlight-color:rgba(0,0,0,0)}td,th{word-wrap:break-word;padding:5px 10px;border:1px solid #DDD;}table{margin-bottom:10px;border-collapse:collapse;display:table;width:100%!important;}.appmsg_skin_default .rich_media_area_primary{background-color:#fff}.appmsg_skin_default .rich_media_area_primary .weui-loadmore_line .weui-loadmore__tips{background-color:#fff}.rich_media_area_primary{padding:20px 16px 12px;background-color:#fafafa}@media (max-width:375px){.rich_media_area_primary{padding:20px 60px 15px 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data={\"mp\":\"\u751f\u4fe1\u679c\",\"title\":\"Cell Ranger\u8f7b\u677e\u641e\u5b9a\u5355\u7ec6\u80de\u4e0a\u6e38\u5206\u6790\",\"time\":\"2023-05-25 19:00:09\",\"timeStamp\":\"1685012409\"};\n<\/script><br \/>\n<body><\/p>\n<div class=\"rich_media\">\n<h1 class=\"rich_media_title\" id=\"activity-name\"><a href=\"http:\/\/mp.weixin.qq.com\/s?__biz=Mzg3OTg3MjQyNg==&mid=2247487779&idx=1&sn=a6c75e79c5c54c9a71657c5944e4391f&chksm=cf7c81e6f80b08f0d1fcbbe32b074ca2998659846ce95ad3e989459796e3f6edd581dec2bdbe#rd\" target=\"_blank\" rel=\"noopener\">Cell Ranger\u8f7b\u677e\u641e\u5b9a\u5355\u7ec6\u80de\u4e0a\u6e38\u5206\u6790<\/a><\/h1>\n<div id=\"meta_content\" class=\"rich_media_meta_list\"><span id=\"copyright_logo\" class=\"wx_tap_link js_wx_tap_highlight rich_media_meta icon_appmsg_tag appmsg_title_tag weui-wa-hotarea\">\u539f\u521b <\/span><span class=\"rich_media_meta rich_media_meta_text\">\u5c0f\u679c <\/span><span class=\"rich_media_meta rich_media_meta_nickname\" id=\"profileBt\"><a href=\"javascript:void(0);\" class=\"wx_tap_link js_wx_tap_highlight weui-wa-hotarea\" id=\"js_name\">\u751f\u4fe1\u679c <\/a><\/span><em id=\"publish_time\" class=\"rich_media_meta rich_media_meta_text\">2023-05-25 19:00:09<\/em><\/div>\n<p><content><\/p>\n<section data-role=\"outer\" label=\"edit by 135editor\">\n<section>\n<section>\n<section>\n<section>\n<section>\n<section>\n<section data-width=\"100%\" style=\"font-size: 16px;letter-spacing: 0.578px;width: 100%;flex: 0 0 100%;opacity: 1;\">\n<section style=\"line-height: 1.8;\">\n<section>\n<section>\n<section style=\"margin-top: 10px;margin-bottom: 20px;display: flex;flex-flow: row nowrap;text-align: center;justify-content: center;\">\n<section style=\"display: inline-block;width: 100%;vertical-align: top;border-style: solid;border-width: 1px;border-color: rgb(67, 67, 67);flex: 0 0 auto;align-self: flex-start;height: auto;box-shadow: rgb(255, 219, 118) 6px 6px 0px;background-color: rgb(255, 255, 255);\">\n<section style=\"text-align: left;justify-content: flex-start;display: flex;flex-flow: row nowrap;\">\n<section style=\"display: inline-block;width: 70%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 70% !important;\">\n<section style=\"margin-top: 10px;\">\n<section style=\"text-align: center;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u751f\u4fe1\u4ebaR\u8bed\u8a00\u5b66\u4e60\u5fc5\u5907<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u7acb\u523b\u62e5\u6709\u4e00\u4e2aRstudio\u8d26\u53f7<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\"><strong><span style=\"font-size: 15px;\">\u5f00\u542f\u5347\u7ea7\u6a21\u5f0f\u5427<\/span><\/strong><\/span><\/p>\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"color: rgb(255, 129, 36);font-size: 12px;letter-spacing: 0.5px;\">\uff0856\u7ebf\u7a0b\uff0c256G\u5185\u5b58\uff0c\u4e2a\u4eba\u5b58\u50a81T\uff09<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"display: inline-block;width: 30%;vertical-align: top;align-self: flex-start;flex: 0 0 auto;height: auto;max-width: 30% !important;\">\n<section style=\"margin-top: 10px;margin-bottom: 10px;text-align: center;line-height: 0;\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-cropselx1=\"0\" data-cropselx2=\"162\" data-cropsely1=\"0\" data-cropsely2=\"162\" data-ratio=\"1\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/1_ib2l1ye6HNIkwTG696C2pf9yAtdeGA-40.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyB69UyXDLG0wQcISNwmL6DlpIKVBnCSOXHTWJhLcxic2qtibaib2l1ye6HNIkwTG696C2pf9yAtdeGA\/640?wx_fmt=png'\" data-type=\"jpeg\" data-w=\"400\" style=\"height: 111px;vertical-align: middle;width: 111px;\" data-recalc-dims=\"1\"><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-role=\"list\">\n<ul class=\"list-paddingleft-1\" style=\"font-size: 16px;letter-spacing: 0.578px;padding-left: 30px;width: 100%;list-style-position: outside;\">\n<li>\n<p style=\"text-align:justify;text-indent: 0em;line-height: 1.75em;\"><span style=\"font-size: 14px;letter-spacing: 0.5px;line-height: 2em;caret-color: rgb(255, 0, 0);font-family: mp-quote, -apple-system-font, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;\">\u53c8\u4e00\u6b21\uff0c\u5c0f\u679c\u51c6\u65f6\u4e0e\u5927\u5bb6\u76f8\u89c1\u5566\u3002\u4eca\u5929\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u5b66\u4e60\u5355\u7ec6\u80de\u4e0a\u6e38\u5206\u6790\u6d41\u7a0b\u5427\u3002<\/span><\/p>\n<p style=\"text-align:justify;text-indent: 0em;line-height: 1.75em;\"><br \/><\/p>\n<\/li>\n<\/ul>\n<section style=\"font-size: 16px;letter-spacing: 0.578px;height: 0px;overflow: hidden;\"><br \/><\/section>\n<section style=\"font-size: 16px;letter-spacing: 0.578px;height: 0px;overflow: hidden;\"><br \/><\/section>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u5355\u7ec6\u80de\u6d4b\u5e8f\u4e0a\u6e38\u5206\u6790\u4e3b\u8981\u4f7f\u7528Cell Ranger\u8f6f\u4ef6\u3002Cell Ranger \u662f\u4e00\u4e2a\u7528\u4e8e\u5355\u7ec6\u80de\u57fa\u56e0\u8868\u8fbe\u5206\u6790\u7684\u8f6f\u4ef6\u5305\uff0c\u7531 10x Genomics \u516c\u53f8\u5f00\u53d1\u3002\u5b83\u5305\u542b\u4e94\u4e2a\u4e0e3’\u5355\u7ec6\u80de\u57fa\u56e0\u8868\u8fbe\u65b9\u6848\u53ca\u76f8\u5173\u4ea7\u54c1\u76f8\u5173\u7684\u6d41\u7a0b\uff1acellranger mkfastq\u3001cellranger count\u3001cellranger aggr\u3001cellranger reanalyze \u548c cellranger vdj\u3002\u5176\u4e2d\uff0ccellranger mkfastq \u7684\u4f5c\u7528\u662f\u5c06Illumina\u6d4b\u5e8f\u4eea\u751f\u6210\u7684\u539f\u59cbbase call\uff08BCL\uff09\u6587\u4ef6\u89e3\u6790\u6210FASTQ\u683c\u5f0f\u7684\u6587\u4ef6\u3002\u5b83\u662fIllumina\u7684bcl2fastq\u7684\u5c01\u88c5\uff0c\u5e76\u5e26\u6709\u7279\u5b9a\u4e8e10x Genomics\u6587\u5e93\u7684\u9644\u52a0\u529f\u80fd\u3002<\/span><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u6211\u4eec\u53ef\u4ee5\u4ece10x Genomics\u7684\u5b98\u65b9\u7f51\u7ad9\u4e0a\u4e0b\u8f7d\u548c\u5b89\u88c5Cell Ranger\u8f6f\u4ef6\uff0c\u5177\u4f53\u8f6f\u4ef6\u4f7f\u7528\u53ef\u4ee5\u53c2\u8003\u5b98\u7f51<strong><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);color: rgb(61, 170, 214);\">https:\/\/support.10xgenomics.com\/single-cell-gene-expression\/software\/pipelines\/latest\/what-is-cell-ranger\u3002<\/span><\/strong><\/span><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u6574\u4e2a\u5355\u7ec6\u80de\u4e0a\u6e38\u6d41\u7a0b\u548ccell Ranger\u7684\u4f7f\u7528\u5982\u56fe\u6240\u793a\u3002<\/span><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.26908396946564883\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ZJqhMzfeib8WwX6wnEY5B8sGX2obPQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNUZQLIOlY08eCfBltibqb1YuCaxZJqhMzfeib8WwX6wnEY5B8sGX2obPQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"524\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u5c0f\u679c\u662f\u6309\u7167\u4ee5\u4e0b\u6d41\u7a0b\u6765\u64cd\u4f5c\u7684\uff1a<\/span><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\"><br \/><\/span><\/p>\n<section style=\"font-size: 16px;\">\n<section style=\"line-height: 0;text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-backh=\"58\" data-backw=\"116\" data-ratio=\"0.5\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_QiaOCcR0jFpvjkSAu3UmKL82ohCV5Q-10.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNXhQ4GD7nqK0jxIA9vNfaZMfcibQiaOCcR0jFpvjkSAu3UmKL82ohCV5Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;height: auto;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 20px;\" powered-by=\"xiumi.us\">\n<p><em><strong>\u8f6f\u4ef6\u4e0b\u8f7d<\/strong><\/em><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">mkdir yard #\u65b0\u5efa\u6587\u4ef6\u5939<\/span><\/code><code><span class=\"code-snippet_outer\">cd ..\/yard #\u8fdb\u5165\u6b64\u6587\u4ef6\u5939<\/span><\/code><code><span class=\"code-snippet_outer\">mkdir apps<\/span><\/code><code><span class=\"code-snippet_outer\">cd apps<\/span><\/code><code><span class=\"code-snippet_outer\">#\u4e0b\u8f7dcellranger\u8f6f\u4ef6\u5e76\u89e3\u538b<\/span><\/code><code><span class=\"code-snippet_outer\">curl -o cellranger<span class=\"code-snippet__number\">-7.1<\/span><span class=\"code-snippet__number\">.0<\/span>.tar.gz <span class=\"code-snippet__string\">\"https:\/\/cf.10xgenomics.com\/releases\/cell-exp\/cellranger-7.1.0.tar.gz?Expires=1680536714&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cHM6Ly9jZi4xMHhnZW5vbWljcy5jb20vcmVsZWFzZXMvY2VsbC1leHAvY2VsbHJhbmdlci03LjEuMC50YXIuZ3oiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE2ODA1MzY3MTR9fX1dfQ__&Signature=nrDGafilO0qCsE0KPOKhyFZPdj~go-zAZhACPT6v~Rjd9fPibaE28B22726ytq1WZNJfwBysfQMI3Xo3zEbjc8gJZv-141alIGts5eyXj-JpMgu6mxVPJQ3jKMopkP~B6vNyOR1R9h5IIccHZD~RlKL0wT-cXDgefvJoXoqmx0Lxt6Jpvuoekm0h2l~AKF~m4ARSItKFeQ-W2OxF2BOaMlyXIYPYOhcESApA9TabRqFUnhGUssld1nJdfSfGR-uFHH05AxUK6D1~LtTO5whUNUib8FHsYRwdzieFjy-Xc7i7KPcvPGwnUecn4RnC4gPBlJ3oBmEArTQedRE4rlTtWA__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tar -zxvf cellranger<span class=\"code-snippet__number\">-7.1<\/span><span class=\"code-snippet__number\">.0<\/span>.tar.gz #\u89e3\u538b<\/span><\/code><code><span class=\"code-snippet_outer\">#\u4e3a\u65b9\u4fbf\u4f7f\u7528\uff0c\u5c06\u8f6f\u4ef6\u8def\u5f84\u8bbe\u7f6e\u4e3a\u53d8\u91cfPATH<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">export<\/span> PATH=\/mnt\/home\/user.name\/yard\/apps\/cellranger<span class=\"code-snippet__number\">-6.1<\/span><span class=\"code-snippet__number\">.2<\/span>:$PATH<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" data-ratio=\"0.5\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_s2ZHCtbN9nDKgpfniawYJJzqxT6v6g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNq0nuSrPNnVriasrjcop8ONDW3ss2ZHCtbN9nDKgpfniawYJJzqxT6v6g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 20px;\" powered-by=\"xiumi.us\">\n<p><em><strong>\u51c6\u5907fastq\u6587\u4ef6\u548c\u53c2\u8003\u57fa<\/strong><\/em><\/p>\n<p><em><strong><br \/><\/strong><\/em><\/p>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p style=\"text-align: left;\"><em><strong><span style=\"text-align: unset;font-size: 18px;\">1.\u4e0b\u8f7d\u53c2\u8003<\/span><\/strong><\/em><strong><em><span style=\"font-size: 18px;color: rgb(62, 62, 62);\">\u57fa\u56e0<\/span><\/em><\/strong><em><strong><span style=\"text-align: unset;font-size: 18px;\">\u7ec4\u6570\u636e\uff1a<\/span><\/strong><\/em><\/p>\n<p><span style=\"font-size: 14px;\">\u53ef\u76f4\u63a5\u4e0b\u8f7d\u5b98\u7f51\u63d0\u4f9b\u7684\u5df2\u6784\u5efa\u597d\u7684\u7d22\u5f15\u6587\u4ef6\uff0chttps:\/\/www.10xgenomics.com\/resources\/datasets\/ \uff0c\u5efa\u8bae\u4e0b\u8f7d\u6700\u65b0\u7248\u672c\u5e76\u8fdb\u884c\u89e3\u538b\u3002<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">wget https:\/\/cf.10xgenomics.com\/supp\/cell-exp\/refdata-gex-GRCh38-2020-A.tar.gz tar -zxvf refdata-gex-GRCh38-2020-A.tar.gz<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><strong style=\"text-align: left;\"><em><span style=\"font-size: 18px;\">2.fastq\u6587\u4ef6<\/span><\/em><\/strong><br \/><\/p>\n<p><span style=\"font-size: 14px;\">\u82e5\u662fBCL\u539f\u59cb\u7684\u6d4b\u5e8f\u6570\u636e\uff0c\u987b\u4f7f\u7528cellranger mkfastq\u5c06\u5176\u8f6c\u6362\u4e3afastq\u683c\u5f0f\u6587\u4ef6\u3002<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">cellranger mkfastq --id=tutorial_walk_through #\u8f93\u51fa\u6587\u4ef6\u5939<\/span><\/code><code><span class=\"code-snippet_outer\">--run=\/mnt\/home\/user.name\/yard\/run_cellranger_mkfastq\/cellranger-tiny-bcl-1.2.0 #BCL\u6587\u4ef6\u6587\u4ef6\u5939<\/span><\/code><code><span class=\"code-snippet_outer\">--csv=\/mnt\/home\/user.name\/yard\/run_cellranger_mkfastq\/cellranger-tiny-bcl-simple-1.2.0.c #csv\u6587\u4ef6<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">\u82e5\u662ffastq\u6587\u4ef6\uff0c\u53ef\u76f4\u63a5run cellranger count\u8fdb\u884c\u5b9a\u91cf\uff0c\u5f97\u5230\u8868\u8fbe\u77e9\u9635\u3002\u5982\u679c\u6709\u591a\u4e2a\u751f\u7269\u5b66\u6837\u672c\u6216\u4e00\u4e2a\u6837\u672c\u6709\u591a\u4e2a\u91cd\u590d\/\u6587\u5e93\u65f6\uff0c\u53ef\u4ee5\u4f7f\u7528cellranger aggr\u8fdb\u884c\u6574\u5408\u3002<br \/><\/span><\/p>\n<p><span style=\"font-size: 14px;\">fastq\u6587\u4ef6\u5982\u4e0b\u6240\u793a\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">scdata_1k_v3_fastqs\/ scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L001_R2_001.fastq.gz scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L002_I1_001.fastq.gz scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L001_R1_001.fastq.gz scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L002_R1_001.fastq.gz scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L002_R2_001.fastq.gz scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L001_I1_001.fastq.gz<\/span><\/code><code><span class=\"code-snippet_outer\">#I1 Index<\/span><\/code><code><span class=\"code-snippet_outer\">#R1 barcode+UMI<\/span><\/code><code><span class=\"code-snippet_outer\">#R2 reads<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.49899799599198397\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_PSgMgn9cx3xIMRpoK7HUMUxLr0HL3A-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNszG7picpYriceh3kdysIicAjyUtPSgMgn9cx3xIMRpoK7HUMUxLr0HL3A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"499\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 20px;\" powered-by=\"xiumi.us\">\n<p><em><strong>\u8fd0\u884ccellranger<\/strong><\/em><\/p>\n<p><em><strong><br \/><\/strong><\/em><\/p>\n<\/section>\n<section style=\"text-align: unset;font-size: 18px;\" powered-by=\"xiumi.us\">\n<p><em><strong>1.cellranger-count<\/strong><\/em><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">Count gene expression (targeted or whole-transcriptome) and\/or feature barcode reads from a single sample and GEM well<\/span><\/code><code><span class=\"code-snippet_outer\">cellranger count --id=run_count_1kscdatas #\u8f93\u51fa\u6587\u4ef6\u5939\u7684\u540d\u5b57 --fastqs=\/mnt\/home\/user.name\/yard\/run_cellranger_count\/scdata_1k_v3_fastqs #\u6d4b\u5e8f\u6570\u636e\u7684\u8def\u5f84<\/span><\/code><code><span class=\"code-snippet_outer\">--sample=scdata_1k_v3 #\u6307\u5b9asample\u7684\u914d\u5957\u6587\u4ef6\u524d\u7f00 --transcriptome=\/mnt\/home\/user.name\/yard\/run_cellranger_count\/refdata-gex-GRCh38-2020-A #\u53c2\u8003\u57fa\u56e0\u7ec4\u8def\u5f84<\/span><\/code><code><span class=\"code-snippet_outer\">cellrangercount.sh<\/span><\/code><code><span class=\"code-snippet_outer\">cellranger=..\/cellranger-6.1.2\/bin\/cellranger<\/span><\/code><code><span class=\"code-snippet_outer\">db=..\/refdata-gex-GRCh38-2020-A<\/span><\/code><code><span class=\"code-snippet_outer\">fq_dir=..\/fastq\/<\/span><\/code><code><span class=\"code-snippet_outer\">$cellranger count --id=test1 #\u8f93\u51fa\u6587\u4ef6\u5939\u7684\u540d\u5b57<\/span><\/code><code><span class=\"code-snippet_outer\">--fastqs=$fq_dir #\u6d4b\u5e8f\u6570\u636e\u7684\u8def\u5f84<\/span><\/code><code><span class=\"code-snippet_outer\">--sample=scdata_1k_v3 #\u6307\u5b9asample\u7684\u914d\u5957\u6587\u4ef6\u524d\u7f00<\/span><\/code><code><span class=\"code-snippet_outer\">--transcriptome=$db #\u53c2\u8003\u57fa\u56e0\u7ec4\u8def\u5f84<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;font-size: 18px;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p style=\"text-align: left;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">2.cellranger aggr<\/span><\/em><\/strong><\/p>\n<p><span style=\"font-size: 14px;\"><strong>\u2460Create aggregation CSV<\/strong><\/span><\/p>\n<p><span style=\"font-size: 14px;\">The CSV file is a two-column file. The first column is for the sample id. This id name can be anything you want. Choose descriptive ids since they are used later in the analysis. The second column contains the paths to themolecule_info.h5 output files from the cellranger count pipelines.<\/span><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.17889908256880735\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_X38lKrrZuVe8ibLg8EEjFqfYtFN0YA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtN0ouKkQfqb0IUibdc1v5XWPdh43X38lKrrZuVe8ibLg8EEjFqfYtFN0YA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"436\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"font-size: 14px;text-align: unset;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><strong>\u2461\u8fd0\u884c\u4ee3\u7801<\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">cellranger aggr --id=1k_10k_scdata_aggr<\/span><\/code><code><span class=\"code-snippet_outer\">--csv=scdata_aggr.csv<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">Cellranger\u7684\u6d41\u7a0b\u5c31\u5982\u4e0a\u6240\u793a\uff0c\u5927\u5bb6\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u5b9e\u8df5\u4e00\u4e0b\u5427\u3002<br \/><\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u6211\u4eec\u5bf9\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u5206\u6790\u65f6\uff0c\u5fc5\u5b9a\u4f1a\u7528\u5230\u6bd4\u5bf9\u8f6f\u4ef6\u6216\u8005\u5de5\u5177\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u7ed9\u5927\u5bb6\u63a8\u8350\u4e00\u4e2a\u5728\u7ebf\u5c0f\u5de5\u5177\uff1afasta\u5e8f\u5217\u591a\u91cd\u6bd4\u5bf9\uff08http:\/\/www.biocloudservice.com\/321\/321.php\uff09\uff0c\u652f\u6301\u8f93\u5165\u6570\u636e\uff0c\u5feb\u901f\u5f97\u5230\u7ed3\u679c\u3002\u5927\u5bb6\u5728\u4e4b\u540e\u6bd4\u5bf9\u65f6\u53ef\u4ee5\u7528\u8d77\u6765\u54e6\u3002<\/span><span style=\"font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);text-align: unset;\"><\/span><\/p>\n<\/section>\n<\/section>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><br \/><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u597d\u5566\uff0c\u4e0d\u591a\u8bf4\u4e86\uff0c\u4eca\u5929\u7684\u5185\u5bb9\u5c31\u5230\u8fd9\u91cc\u4e86\uff0c\u4f60\u5b66\u4f1a\u4e86\u5417\uff01<\/span><span style=\"font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\"><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-tools=\"135\u7f16\u8f91\u5668\" data-id=\"105054\" style=\"font-size: 16px;\">\n<section style=\"margin: 10px auto;text-align: center;\">\n<section style=\"padding-top: 30px;padding-bottom: 30px;background-color: rgb(242, 246, 255);border-radius: 7px;\">\n<section style=\"display: flex;justify-content: space-evenly;align-items: center;\">\n<section data-width=\"26%\" style=\"width: 26%;max-width: 26% !important;\">\n<section style=\"padding: 7px;border-radius: 15px;box-shadow: rgba(169, 187, 223, 0.45) 4px 4px 8px, rgb(255, 255, 255) -2.5px -2.5px 5px;\">\n<section data-width=\"100%\" style=\"width: 100%;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.005281690140845\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_0WFLKBMicbm6iawtkrNrMxpSVU9GBQ-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtN261llpmfF6btPBTUKkibEdnRz5Y0WFLKBMicbm6iawtkrNrMxpSVU9GBQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"568\" data-width=\"100%\" style=\"vertical-align: inherit;width: 100%;display: block;border-radius: 7px;\" title=\"\u5c0f\u4e91-\u5fae\u4fe1\u4e8c\u7ef4\u7801.png\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<section data-width=\"62%\" style=\"width: 62%;max-width: 62% !important;\">\n<section style=\"display: inline-block;\">\n<section style=\"padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section data-brushtype=\"text\" style=\"font-size: 14px;letter-spacing: 1.5px;color: rgb(111, 133, 172);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u5fae\u4fe1\u53f7 | 18502195490<\/span><\/p>\n<\/section>\n<\/section>\n<section style=\"margin-top: 12px;padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section data-brushtype=\"text\" style=\"font-size: 14px;letter-spacing: 1.5px;color: rgb(111, 133, 172);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u77e5\u4e4e | \u751f\u4fe1\u679c<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"letter-spacing: 0.578px;caret-color: rgba(0, 0, 0, 0);font-size: 16px;\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 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onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAyB69UyXDLG0wQcISNwmL6DlpIKVBnCSOXHTWJhLcxic2qtibaib2l1ye6HNIkwTG696C2pf9yAtdeGA\/640?wx_fmt=png'\" data-type=\"jpeg\" data-w=\"400\" style=\"height: 111px;vertical-align: middle;width: 111px;\" data-recalc-dims=\"1\"><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-role=\"list\">\n<ul class=\"list-paddingleft-1\" style=\"font-size: 16px;letter-spacing: 0.578px;padding-left: 30px;width: 100%;list-style-position: outside;\">\n<li>\n<p style=\"text-align:justify;text-indent: 0em;line-height: 1.75em;\"><span style=\"font-size: 14px;letter-spacing: 0.5px;line-height: 2em;caret-color: rgb(255, 0, 0);font-family: mp-quote, -apple-system-font, BlinkMacSystemFont, "Helvetica Neue", "PingFang SC", "Hiragino Sans GB", "Microsoft YaHei UI", "Microsoft YaHei", Arial, sans-serif;\">\u53c8\u4e00\u6b21\uff0c\u5c0f\u679c\u51c6\u65f6\u4e0e\u5927\u5bb6\u76f8\u89c1\u5566\u3002\u4eca\u5929\u548c\u5c0f\u679c\u4e00\u8d77\u6765\u5b66\u4e60\u5355\u7ec6\u80de\u4e0a\u6e38\u5206\u6790\u6d41\u7a0b\u5427\u3002<\/span><\/p>\n<p style=\"text-align:justify;text-indent: 0em;line-height: 1.75em;\"><br \/><\/p>\n<\/li>\n<\/ul>\n<section style=\"font-size: 16px;letter-spacing: 0.578px;height: 0px;overflow: hidden;\"><br \/><\/section>\n<section style=\"font-size: 16px;letter-spacing: 0.578px;height: 0px;overflow: hidden;\"><br \/><\/section>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u5355\u7ec6\u80de\u6d4b\u5e8f\u4e0a\u6e38\u5206\u6790\u4e3b\u8981\u4f7f\u7528Cell Ranger\u8f6f\u4ef6\u3002Cell Ranger \u662f\u4e00\u4e2a\u7528\u4e8e\u5355\u7ec6\u80de\u57fa\u56e0\u8868\u8fbe\u5206\u6790\u7684\u8f6f\u4ef6\u5305\uff0c\u7531 10x Genomics \u516c\u53f8\u5f00\u53d1\u3002\u5b83\u5305\u542b\u4e94\u4e2a\u4e0e3’\u5355\u7ec6\u80de\u57fa\u56e0\u8868\u8fbe\u65b9\u6848\u53ca\u76f8\u5173\u4ea7\u54c1\u76f8\u5173\u7684\u6d41\u7a0b\uff1acellranger mkfastq\u3001cellranger count\u3001cellranger aggr\u3001cellranger reanalyze \u548c cellranger vdj\u3002\u5176\u4e2d\uff0ccellranger mkfastq \u7684\u4f5c\u7528\u662f\u5c06Illumina\u6d4b\u5e8f\u4eea\u751f\u6210\u7684\u539f\u59cbbase call\uff08BCL\uff09\u6587\u4ef6\u89e3\u6790\u6210FASTQ\u683c\u5f0f\u7684\u6587\u4ef6\u3002\u5b83\u662fIllumina\u7684bcl2fastq\u7684\u5c01\u88c5\uff0c\u5e76\u5e26\u6709\u7279\u5b9a\u4e8e10x Genomics\u6587\u5e93\u7684\u9644\u52a0\u529f\u80fd\u3002<\/span><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u6211\u4eec\u53ef\u4ee5\u4ece10x Genomics\u7684\u5b98\u65b9\u7f51\u7ad9\u4e0a\u4e0b\u8f7d\u548c\u5b89\u88c5Cell Ranger\u8f6f\u4ef6\uff0c\u5177\u4f53\u8f6f\u4ef6\u4f7f\u7528\u53ef\u4ee5\u53c2\u8003\u5b98\u7f51<strong><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);color: rgb(61, 170, 214);\">https:\/\/support.10xgenomics.com\/single-cell-gene-expression\/software\/pipelines\/latest\/what-is-cell-ranger\u3002<\/span><\/strong><\/span><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u6574\u4e2a\u5355\u7ec6\u80de\u4e0a\u6e38\u6d41\u7a0b\u548ccell Ranger\u7684\u4f7f\u7528\u5982\u56fe\u6240\u793a\u3002<\/span><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;text-align: center;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-galleryid=\"\" data-ratio=\"0.26908396946564883\" data-s=\"300,640\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/2_ZJqhMzfeib8WwX6wnEY5B8sGX2obPQ.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNUZQLIOlY08eCfBltibqb1YuCaxZJqhMzfeib8WwX6wnEY5B8sGX2obPQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"524\" style=\"\" data-recalc-dims=\"1\"><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u5c0f\u679c\u662f\u6309\u7167\u4ee5\u4e0b\u6d41\u7a0b\u6765\u64cd\u4f5c\u7684\uff1a<\/span><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\"><br \/><\/span><\/p>\n<section style=\"font-size: 16px;\">\n<section style=\"line-height: 0;text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-backh=\"58\" data-backw=\"116\" data-ratio=\"0.5\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/3_QiaOCcR0jFpvjkSAu3UmKL82ohCV5Q-10.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNXhQ4GD7nqK0jxIA9vNfaZMfcibQiaOCcR0jFpvjkSAu3UmKL82ohCV5Q\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;height: auto;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 20px;\" powered-by=\"xiumi.us\">\n<p><em><strong>\u8f6f\u4ef6\u4e0b\u8f7d<\/strong><\/em><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">mkdir yard #\u65b0\u5efa\u6587\u4ef6\u5939<\/span><\/code><code><span class=\"code-snippet_outer\">cd ..\/yard #\u8fdb\u5165\u6b64\u6587\u4ef6\u5939<\/span><\/code><code><span class=\"code-snippet_outer\">mkdir apps<\/span><\/code><code><span class=\"code-snippet_outer\">cd apps<\/span><\/code><code><span class=\"code-snippet_outer\">#\u4e0b\u8f7dcellranger\u8f6f\u4ef6\u5e76\u89e3\u538b<\/span><\/code><code><span class=\"code-snippet_outer\">curl -o cellranger<span class=\"code-snippet__number\">-7.1<\/span><span class=\"code-snippet__number\">.0<\/span>.tar.gz <span class=\"code-snippet__string\">\"https:\/\/cf.10xgenomics.com\/releases\/cell-exp\/cellranger-7.1.0.tar.gz?Expires=1680536714&Policy=eyJTdGF0ZW1lbnQiOlt7IlJlc291cmNlIjoiaHR0cHM6Ly9jZi4xMHhnZW5vbWljcy5jb20vcmVsZWFzZXMvY2VsbC1leHAvY2VsbHJhbmdlci03LjEuMC50YXIuZ3oiLCJDb25kaXRpb24iOnsiRGF0ZUxlc3NUaGFuIjp7IkFXUzpFcG9jaFRpbWUiOjE2ODA1MzY3MTR9fX1dfQ__&Signature=nrDGafilO0qCsE0KPOKhyFZPdj~go-zAZhACPT6v~Rjd9fPibaE28B22726ytq1WZNJfwBysfQMI3Xo3zEbjc8gJZv-141alIGts5eyXj-JpMgu6mxVPJQ3jKMopkP~B6vNyOR1R9h5IIccHZD~RlKL0wT-cXDgefvJoXoqmx0Lxt6Jpvuoekm0h2l~AKF~m4ARSItKFeQ-W2OxF2BOaMlyXIYPYOhcESApA9TabRqFUnhGUssld1nJdfSfGR-uFHH05AxUK6D1~LtTO5whUNUib8FHsYRwdzieFjy-Xc7i7KPcvPGwnUecn4RnC4gPBlJ3oBmEArTQedRE4rlTtWA__&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA\"<\/span><\/span><\/code><code><span class=\"code-snippet_outer\">tar -zxvf cellranger<span class=\"code-snippet__number\">-7.1<\/span><span class=\"code-snippet__number\">.0<\/span>.tar.gz #\u89e3\u538b<\/span><\/code><code><span class=\"code-snippet_outer\">#\u4e3a\u65b9\u4fbf\u4f7f\u7528\uff0c\u5c06\u8f6f\u4ef6\u8def\u5f84\u8bbe\u7f6e\u4e3a\u53d8\u91cfPATH<\/span><\/code><code><span class=\"code-snippet_outer\"><span class=\"code-snippet__keyword\">export<\/span> PATH=\/mnt\/home\/user.name\/yard\/apps\/cellranger<span class=\"code-snippet__number\">-6.1<\/span><span class=\"code-snippet__number\">.2<\/span>:$PATH<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" data-ratio=\"0.5\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/4_s2ZHCtbN9nDKgpfniawYJJzqxT6v6g.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNq0nuSrPNnVriasrjcop8ONDW3ss2ZHCtbN9nDKgpfniawYJJzqxT6v6g\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"500\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 20px;\" powered-by=\"xiumi.us\">\n<p><em><strong>\u51c6\u5907fastq\u6587\u4ef6\u548c\u53c2\u8003\u57fa<\/strong><\/em><\/p>\n<p><em><strong><br \/><\/strong><\/em><\/p>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p style=\"text-align: left;\"><em><strong><span style=\"text-align: unset;font-size: 18px;\">1.\u4e0b\u8f7d\u53c2\u8003<\/span><\/strong><\/em><strong><em><span style=\"font-size: 18px;color: rgb(62, 62, 62);\">\u57fa\u56e0<\/span><\/em><\/strong><em><strong><span style=\"text-align: unset;font-size: 18px;\">\u7ec4\u6570\u636e\uff1a<\/span><\/strong><\/em><\/p>\n<p><span style=\"font-size: 14px;\">\u53ef\u76f4\u63a5\u4e0b\u8f7d\u5b98\u7f51\u63d0\u4f9b\u7684\u5df2\u6784\u5efa\u597d\u7684\u7d22\u5f15\u6587\u4ef6\uff0chttps:\/\/www.10xgenomics.com\/resources\/datasets\/ \uff0c\u5efa\u8bae\u4e0b\u8f7d\u6700\u65b0\u7248\u672c\u5e76\u8fdb\u884c\u89e3\u538b\u3002<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">wget https:\/\/cf.10xgenomics.com\/supp\/cell-exp\/refdata-gex-GRCh38-2020-A.tar.gz tar -zxvf refdata-gex-GRCh38-2020-A.tar.gz<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><strong style=\"text-align: left;\"><em><span style=\"font-size: 18px;\">2.fastq\u6587\u4ef6<\/span><\/em><\/strong><br \/><\/p>\n<p><span style=\"font-size: 14px;\">\u82e5\u662fBCL\u539f\u59cb\u7684\u6d4b\u5e8f\u6570\u636e\uff0c\u987b\u4f7f\u7528cellranger mkfastq\u5c06\u5176\u8f6c\u6362\u4e3afastq\u683c\u5f0f\u6587\u4ef6\u3002<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">cellranger mkfastq --id=tutorial_walk_through #\u8f93\u51fa\u6587\u4ef6\u5939<\/span><\/code><code><span class=\"code-snippet_outer\">--run=\/mnt\/home\/user.name\/yard\/run_cellranger_mkfastq\/cellranger-tiny-bcl-1.2.0 #BCL\u6587\u4ef6\u6587\u4ef6\u5939<\/span><\/code><code><span class=\"code-snippet_outer\">--csv=\/mnt\/home\/user.name\/yard\/run_cellranger_mkfastq\/cellranger-tiny-bcl-simple-1.2.0.c #csv\u6587\u4ef6<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">\u82e5\u662ffastq\u6587\u4ef6\uff0c\u53ef\u76f4\u63a5run cellranger count\u8fdb\u884c\u5b9a\u91cf\uff0c\u5f97\u5230\u8868\u8fbe\u77e9\u9635\u3002\u5982\u679c\u6709\u591a\u4e2a\u751f\u7269\u5b66\u6837\u672c\u6216\u4e00\u4e2a\u6837\u672c\u6709\u591a\u4e2a\u91cd\u590d\/\u6587\u5e93\u65f6\uff0c\u53ef\u4ee5\u4f7f\u7528cellranger aggr\u8fdb\u884c\u6574\u5408\u3002<br \/><\/span><\/p>\n<p><span style=\"font-size: 14px;\">fastq\u6587\u4ef6\u5982\u4e0b\u6240\u793a\uff1a<\/span><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">scdata_1k_v3_fastqs\/ scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L001_R2_001.fastq.gz scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L002_I1_001.fastq.gz scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L001_R1_001.fastq.gz scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L002_R1_001.fastq.gz scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L002_R2_001.fastq.gz scdata_1k_v3_fastqs\/scdata_1k_v3_S1_L001_I1_001.fastq.gz<\/span><\/code><code><span class=\"code-snippet_outer\">#I1 Index<\/span><\/code><code><span class=\"code-snippet_outer\">#R1 barcode+UMI<\/span><\/code><code><span class=\"code-snippet_outer\">#R2 reads<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<\/section>\n<section style=\"line-height: 0;text-align: center;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;width: 20%;height: auto;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.49899799599198397\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/5_PSgMgn9cx3xIMRpoK7HUMUxLr0HL3A-3.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtNszG7picpYriceh3kdysIicAjyUtPSgMgn9cx3xIMRpoK7HUMUxLr0HL3A\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"499\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"text-align: center;font-size: 20px;\" powered-by=\"xiumi.us\">\n<p><em><strong>\u8fd0\u884ccellranger<\/strong><\/em><\/p>\n<p><em><strong><br \/><\/strong><\/em><\/p>\n<\/section>\n<section style=\"text-align: unset;font-size: 18px;\" powered-by=\"xiumi.us\">\n<p><em><strong>1.cellranger-count<\/strong><\/em><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">Count gene expression (targeted or whole-transcriptome) and\/or feature barcode reads from a single sample and GEM well<\/span><\/code><code><span class=\"code-snippet_outer\">cellranger count --id=run_count_1kscdatas #\u8f93\u51fa\u6587\u4ef6\u5939\u7684\u540d\u5b57 --fastqs=\/mnt\/home\/user.name\/yard\/run_cellranger_count\/scdata_1k_v3_fastqs #\u6d4b\u5e8f\u6570\u636e\u7684\u8def\u5f84<\/span><\/code><code><span class=\"code-snippet_outer\">--sample=scdata_1k_v3 #\u6307\u5b9asample\u7684\u914d\u5957\u6587\u4ef6\u524d\u7f00 --transcriptome=\/mnt\/home\/user.name\/yard\/run_cellranger_count\/refdata-gex-GRCh38-2020-A #\u53c2\u8003\u57fa\u56e0\u7ec4\u8def\u5f84<\/span><\/code><code><span class=\"code-snippet_outer\">cellrangercount.sh<\/span><\/code><code><span class=\"code-snippet_outer\">cellranger=..\/cellranger-6.1.2\/bin\/cellranger<\/span><\/code><code><span class=\"code-snippet_outer\">db=..\/refdata-gex-GRCh38-2020-A<\/span><\/code><code><span class=\"code-snippet_outer\">fq_dir=..\/fastq\/<\/span><\/code><code><span class=\"code-snippet_outer\">$cellranger count --id=test1 #\u8f93\u51fa\u6587\u4ef6\u5939\u7684\u540d\u5b57<\/span><\/code><code><span class=\"code-snippet_outer\">--fastqs=$fq_dir #\u6d4b\u5e8f\u6570\u636e\u7684\u8def\u5f84<\/span><\/code><code><span class=\"code-snippet_outer\">--sample=scdata_1k_v3 #\u6307\u5b9asample\u7684\u914d\u5957\u6587\u4ef6\u524d\u7f00<\/span><\/code><code><span class=\"code-snippet_outer\">--transcriptome=$db #\u53c2\u8003\u57fa\u56e0\u7ec4\u8def\u5f84<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;font-size: 18px;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p style=\"text-align: left;\"><strong><em><span style=\"color: rgb(62, 62, 62);\">2.cellranger aggr<\/span><\/em><\/strong><\/p>\n<p><span style=\"font-size: 14px;\"><strong>\u2460Create aggregation CSV<\/strong><\/span><\/p>\n<p><span style=\"font-size: 14px;\">The CSV file is a two-column file. The first column is for the sample id. This id name can be anything you want. Choose descriptive ids since they are used later in the analysis. The second column contains the paths to themolecule_info.h5 output files from the cellranger count pipelines.<\/span><\/p>\n<\/section>\n<section style=\"line-height: 0;\" powered-by=\"xiumi.us\">\n<section style=\"vertical-align: middle;display: inline-block;line-height: 0;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"0.17889908256880735\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/6_X38lKrrZuVe8ibLg8EEjFqfYtFN0YA.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtN0ouKkQfqb0IUibdc1v5XWPdh43X38lKrrZuVe8ibLg8EEjFqfYtFN0YA\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"436\" style=\"vertical-align: middle;width: 100%;\" data-recalc-dims=\"1\"><\/section>\n<\/section>\n<section style=\"font-size: 14px;text-align: unset;\" powered-by=\"xiumi.us\">\n<p><br \/><\/p>\n<p><strong>\u2461\u8fd0\u884c\u4ee3\u7801<\/strong><\/p>\n<\/section>\n<section class=\"code-snippet__fix code-snippet__js\">\n<ul class=\"code-snippet__line-index code-snippet__js\">\n<li><\/li>\n<li><\/li>\n<\/ul>\n<pre class=\"code-snippet__js\" data-lang=\"c\"><code><span class=\"code-snippet_outer\">cellranger aggr --id=1k_10k_scdata_aggr<\/span><\/code><code><span class=\"code-snippet_outer\">--csv=scdata_aggr.csv<\/span><\/code><\/pre>\n<\/section>\n<section style=\"text-align: unset;\" powered-by=\"xiumi.us\">\n<p><span style=\"font-size: 14px;\">Cellranger\u7684\u6d41\u7a0b\u5c31\u5982\u4e0a\u6240\u793a\uff0c\u5927\u5bb6\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u5b9e\u8df5\u4e00\u4e0b\u5427\u3002<br \/><\/span><\/p>\n<p><span style=\"font-size: 14px;\">\u6211\u4eec\u5bf9\u6d4b\u5e8f\u6570\u636e\u8fdb\u884c\u5206\u6790\u65f6\uff0c\u5fc5\u5b9a\u4f1a\u7528\u5230\u6bd4\u5bf9\u8f6f\u4ef6\u6216\u8005\u5de5\u5177\uff0c\u5c0f\u679c\u5728\u8fd9\u91cc\u7ed9\u5927\u5bb6\u63a8\u8350\u4e00\u4e2a\u5728\u7ebf\u5c0f\u5de5\u5177\uff1afasta\u5e8f\u5217\u591a\u91cd\u6bd4\u5bf9\uff08http:\/\/www.biocloudservice.com\/321\/321.php\uff09\uff0c\u652f\u6301\u8f93\u5165\u6570\u636e\uff0c\u5feb\u901f\u5f97\u5230\u7ed3\u679c\u3002\u5927\u5bb6\u5728\u4e4b\u540e\u6bd4\u5bf9\u65f6\u53ef\u4ee5\u7528\u8d77\u6765\u54e6\u3002<\/span><span style=\"font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);text-align: unset;\"><\/span><\/p>\n<\/section>\n<\/section>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><br \/><\/p>\n<p style=\"font-size: 16px;letter-spacing: 0.578px;\"><span style=\"line-height: 2em;font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\">\u597d\u5566\uff0c\u4e0d\u591a\u8bf4\u4e86\uff0c\u4eca\u5929\u7684\u5185\u5bb9\u5c31\u5230\u8fd9\u91cc\u4e86\uff0c\u4f60\u5b66\u4f1a\u4e86\u5417\uff01<\/span><span style=\"font-size: 14px;letter-spacing: 0.5px;caret-color: rgb(255, 0, 0);\"><\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section data-tools=\"135\u7f16\u8f91\u5668\" data-id=\"105054\" style=\"font-size: 16px;\">\n<section style=\"margin: 10px auto;text-align: center;\">\n<section style=\"padding-top: 30px;padding-bottom: 30px;background-color: rgb(242, 246, 255);border-radius: 7px;\">\n<section style=\"display: flex;justify-content: space-evenly;align-items: center;\">\n<section data-width=\"26%\" style=\"width: 26%;max-width: 26% !important;\">\n<section style=\"padding: 7px;border-radius: 15px;box-shadow: rgba(169, 187, 223, 0.45) 4px 4px 8px, rgb(255, 255, 255) -2.5px -2.5px 5px;\">\n<section data-width=\"100%\" style=\"width: 100%;\"><img decoding=\"async\" class=\"rich_pages wxw-img\" data-ratio=\"1.005281690140845\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/06\/7_0WFLKBMicbm6iawtkrNrMxpSVU9GBQ-1.png?w=640\" onerror=\"this.src='https:\/\/mmbiz.qpic.cn\/mmbiz_png\/zcicibWZessAxec5nH6tybm0EXxCaibxbtN261llpmfF6btPBTUKkibEdnRz5Y0WFLKBMicbm6iawtkrNrMxpSVU9GBQ\/640?wx_fmt=png'\" data-type=\"png\" data-w=\"568\" data-width=\"100%\" style=\"vertical-align: inherit;width: 100%;display: block;border-radius: 7px;\" title=\"\u5c0f\u4e91-\u5fae\u4fe1\u4e8c\u7ef4\u7801.png\" data-recalc-dims=\"1\" \/><\/section>\n<\/section>\n<\/section>\n<section data-width=\"62%\" style=\"width: 62%;max-width: 62% !important;\">\n<section style=\"display: inline-block;\">\n<section style=\"padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section data-brushtype=\"text\" style=\"font-size: 14px;letter-spacing: 1.5px;color: rgb(111, 133, 172);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u5fae\u4fe1\u53f7 | 18502195490<\/span><\/p>\n<\/section>\n<\/section>\n<section style=\"margin-top: 12px;padding: 7px 15px;border-radius: 20px;box-shadow: rgba(169, 187, 223, 0.45) 6px 6px 8px inset, rgb(255, 255, 255) -2.5px -2.5px 5px inset;\">\n<section data-brushtype=\"text\" style=\"font-size: 14px;letter-spacing: 1.5px;color: rgb(111, 133, 172);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u77e5\u4e4e | \u751f\u4fe1\u679c<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"letter-spacing: 0.578px;caret-color: rgba(0, 0, 0, 0);font-size: 16px;\">\n<section>\n<section style=\"margin-top: 0.5em;\">\n<section style=\"padding: 0.5em;border-width: 1px;border-style: solid;box-shadow: rgb(226, 226, 226) 0px 16px 1px -13px;border-color: rgb(0, 150, 136);\">\n<section style=\"text-align: left;\">\n<section style=\"color: rgb(255, 129, 36);text-align: justify;\">\n<section style=\"margin-bottom: 8px;\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u70b9\u51fb<strong><span style=\"color: rgb(0, 150, 136);\">\u201c\u9605\u8bfb\u539f\u6587\u201d<\/span><\/strong>\u7acb\u523b\u62e5\u6709<\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<section style=\"margin-bottom: 8px;font-size: 32px;color: rgb(0, 150, 136);\">\n<p style=\"text-indent: 0em;line-height: 1.75em;\"><span style=\"letter-spacing: 0.5px;\">\u2193\u2193\u2193 <\/span><\/p>\n<\/section>\n<\/section>\n<\/section>\n<\/section>\n<p style=\"display: none;\"><mp-style-type data-value=\"3\"><\/mp-style-type><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<p><\/content><\/p>\n<div class=\"msg_source_url\"><a href=\"http:\/\/www.biocloudservice.com\/home.html\" target=\"_blank\" rel=\"noopener\">\u9605\u8bfb\u539f\u6587<\/a><\/div>\n<\/div>\n<p><\/body><br \/>\n<\/html><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Cell Ranger\u8f7b\u677e\u641e\u5b9a\u5355\u7ec6\u80de\u4e0a\u6e38\u5206\u6790 \u539f\u521b \u5c0f\u679c \u751f\u4fe1\u679c& 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