{"id":66139,"date":"2026-10-15T09:32:07","date_gmt":"2026-10-15T01:32:07","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=66139"},"modified":"2026-10-15T09:32:07","modified_gmt":"2026-10-15T01:32:07","slug":"spaceranger-spatial-transcriptomics-resource-planning","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/spaceranger-spatial-transcriptomics-resource-planning\/","title":{"rendered":"\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u4e00\u4e0a\u673a\u5c31\u7206\u5185\u5b58\uff1fSpace Ranger \u7684 64 GB\u3001128 GB \u548c 1 TB \u8be5\u600e\u4e48\u9009"},"content":{"rendered":"
\n

\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u9879\u76ee\u6700\u5bb9\u6613\u4f4e\u4f30\u7684\uff0c\u4e0d\u662f\u67d0\u6761\u547d\u4ee4\uff0c\u800c\u662f\u6570\u636e\u5728\u540c\u4e00\u6761\u6d41\u7a0b\u91cc\u540c\u65f6\u53e0\u52a0\uff1aFASTQ\u3001\u53c2\u8003\u6587\u4ef6\u3001\u7ec4\u7ec7\u56fe\u50cf\u3001\u6bd4\u5bf9\u4e2d\u95f4\u6587\u4ef6\u3001\u8868\u8fbe\u77e9\u9635\u548c\u4e0b\u6e38\u5bf9\u8c61\u90fd\u8981\u5360\u8d44\u6e90\u3002\u5c0f\u6d4b\u8bd5\u80fd\u8dd1\u901a\uff0c\u4e0d\u4ee3\u8868\u5b8c\u6574\u5207\u7247\u3001\u591a\u6837\u672c\u5e76\u884c\u4e5f\u80fd\u7a33\u5b9a\u5b8c\u6210\u3002<\/p>\n

\u4ee5 10x Genomics \u5f53\u524d Space Ranger v4.1 \u4e3a\u4f8b\uff0c\u5b98\u65b9\u6700\u4f4e\u914d\u7f6e\u662f 8 \u6838 CPU\u300164 GB \u5185\u5b58\u548c 1 TB \u53ef\u7528\u78c1\u76d8<\/strong>\uff0c\u63a8\u8350 32 \u6838\u3001128 GB \u5185\u5b58<\/strong>\u3002\u5b98\u65b9\u8d44\u6e90\u6d4b\u8bd5\u8fd8\u4f7f\u7528\u4e86\u4e00\u4e2a 2.68 \u4ebf reads \u7684 Visium HD \u6570\u636e\u96c6<\/strong>\u3002\u8fd9\u4e9b\u6570\u5b57\u4e0d\u662f\u201c\u8d8a\u5927\u8d8a\u597d\u201d\u7684\u91c7\u8d2d\u53e3\u53f7\uff0c\u800c\u662f\u9879\u76ee\u6392\u961f\u3001\u5e76\u53d1\u548c\u5b58\u50a8\u89c4\u5212\u7684\u8d77\u70b9\u3002<\/p>\n

\"Space
\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u8d44\u6e90\u89c4\u5212\uff1a\u5148\u7528\u5355\u6837\u672c\u5b9e\u6d4b\u5cf0\u503c\uff0c\u518d\u51b3\u5b9a\u591a\u6837\u672c\u5e76\u53d1\u3002<\/figcaption><\/figure>\n

\u5148\u56de\u7b54\u4e00\u4e2a\u5e38\u89c1\u8bef\u533a\uff1aSpace Ranger \u4e00\u5b9a\u8981 GPU \u5417\uff1f<\/h2>\n

\u6807\u51c6 spaceranger count<\/code> \u7684\u6838\u5fc3\u538b\u529b\u901a\u5e38\u5728 CPU\u3001\u5185\u5b58\u3001\u78c1\u76d8\u541e\u5410\u548c\u6587\u4ef6\u7cfb\u7edf\u9650\u5236\uff0c\u5e76\u4e0d\u662f\u5148\u770b\u663e\u5361\u3002GPU \u66f4\u5e38\u51fa\u73b0\u5728\u540e\u7eed\u7684\u56fe\u50cf\u5206\u5272\u3001\u6df1\u5ea6\u5b66\u4e60\u3001\u75c5\u7406\u57fa\u7840\u6a21\u578b\u6216\u67d0\u4e9b\u7a7a\u95f4\u57df\u8bc6\u522b\u65b9\u6cd5\u4e2d\u3002\u53ea\u4e3a\u8dd1\u6807\u51c6\u6d41\u7a0b\u5c31\u5148\u4e70\u9ad8\u7aef GPU\uff0c\u53ef\u80fd\u89e3\u51b3\u4e0d\u4e86\u5185\u5b58\u4e0d\u8db3\u3001\u78c1\u76d8\u5199\u6ee1\u6216 I\/O \u7b49\u5f85\u3002<\/p>\n

\u771f\u6b63\u8981\u505a\u7684\u662f\u628a\u6d41\u7a0b\u62c6\u5f00\uff1a\u539f\u59cb\u6570\u636e\u5904\u7406\u9700\u8981\u591a\u5c11 CPU \u548c\u5185\u5b58\uff1b\u5927\u56fe\u662f\u5426\u4f1a\u62ac\u9ad8\u5cf0\u503c\uff1b\u591a\u4e2a\u6837\u672c\u662f\u5426\u540c\u65f6\u8fd0\u884c\uff1b\u4e0b\u6e38\u662f\u5426\u8fdb\u5165 GPU \u5de5\u5177\u3002\u8d44\u6e90\u8981\u8ddf\u4efb\u52a1\u9636\u6bb5\u5339\u914d\uff0c\u800c\u4e0d\u662f\u53ea\u770b\u4e00\u5f20\u786c\u4ef6\u53c2\u6570\u8868\u3002<\/p>\n

\u4e00\u5f20\u8868\u770b\u6e05\u4e3b\u8981\u74f6\u9888<\/h2>\n
\n\n\n\n\n\n\n\n\n\n\n
\u73af\u8282<\/th>\n\u53ef\u6838\u5bf9\u7684\u6570\u5b57\u6216\u73b0\u8c61<\/th>\n\u66f4\u7a33\u59a5\u7684\u5904\u7406<\/th>\n<\/tr>\n<\/thead>\n
\u57fa\u7840\u8fd0\u884c<\/td>\n\u6700\u4f4e 8 \u6838\u300164 GB\uff1b\u63a8\u8350 32 \u6838\u3001128 GB<\/td>\n\u5148\u5355\u6837\u672c\u8dd1\u901a\uff0c\u518d\u6309\u5cf0\u503c\u51b3\u5b9a\u5e76\u53d1<\/td>\n<\/tr>\n
\u672c\u5730\u8c03\u5ea6<\/td>\n\u9ed8\u8ba4\u7528\u53ef\u7528\u5185\u5b58\u7684 90%\uff0c\u5e76\u4f7f\u7528\u5168\u90e8\u6838\u5fc3<\/td>\n\u663e\u5f0f\u8bbe\u7f6e --localcores<\/code> \u548c --localmem<\/code><\/td>\n<\/tr>\n
\u5b58\u50a8<\/td>\n\u5b98\u65b9\u8981\u6c42 1 TB \u53ef\u7528\u78c1\u76d8<\/td>\n\u539f\u59cb\u3001\u4e34\u65f6\u548c\u7ed3\u679c\u76ee\u5f55\u5206\u5f00\u89c4\u5212<\/td>\n<\/tr>\n
\u5927\u7ec4\u7ec7\u56fe\u50cf<\/td>\n1\u2013100 GB\uff1b64 GB \u5185\u5b58\u4e0a\u9650\u793a\u4f8b\u7ea6 4.5 gigapixels<\/td>\n\u8bb0\u5f55\u50cf\u7d20\u5c3a\u5bf8\u3001\u683c\u5f0f\u3001\u901a\u9053\u6570<\/td>\n<\/tr>\n
\u591a\u6837\u672c\u5e76\u884c<\/td>\n\u5cf0\u503c\u8fd1\u4f3c\u968f\u540c\u65f6\u8fd0\u884c\u4efb\u52a1\u6570\u7d2f\u52a0<\/td>\n\u7ed9\u7cfb\u7edf\u7559 20%\u201325% \u4f59\u91cf<\/td>\n<\/tr>\n
Linux \u6587\u4ef6\u9650\u5236<\/td>\nopen files 16k\uff1buser processes \u6bcf\u6838 64<\/td>\n\u4e0a\u673a\u524d\u68c0\u67e5 ulimit<\/code><\/td>\n<\/tr>\n<\/tbody>\n<\/table><\/div>\n

\u8fd9\u4e9b\u662f\u914d\u7f6e\u8d77\u70b9\uff0c\u4e0d\u662f\u5bf9\u6240\u6709\u6837\u672c\u7684\u8017\u65f6\u4fdd\u8bc1\u3002\u8bfb\u957f\u3001\u6d4b\u5e8f\u6df1\u5ea6\u3001\u56fe\u50cf\u5927\u5c0f\u3001\u662f\u5426\u8f93\u51fa BAM\u3001\u53c2\u8003\u7248\u672c\u548c\u6587\u4ef6\u7cfb\u7edf\u901f\u5ea6\u90fd\u4f1a\u6539\u53d8\u5b9e\u9645\u8868\u73b0\u3002<\/p>\n

\u591a\u6837\u672c\u65f6\uff0c\u522b\u628a\u201c\u80fd\u8dd1\u4e00\u4e2a\u201d\u5f53\u6210\u201c\u80fd\u5e76\u884c\u56db\u4e2a\u201d<\/h2>\n

\u5047\u8bbe\u5355\u4e2a\u4efb\u52a1\u901a\u8fc7\u76d1\u63a7\u53d1\u73b0\u5cf0\u503c\u63a5\u8fd1 96 GB\uff0c\u4e24\u4efb\u52a1\u540c\u65f6\u8fd0\u884c\u7406\u8bba\u4e0a\u5c31\u8981\u7ea6 192 GB\u3002\u518d\u4e3a\u64cd\u4f5c\u7cfb\u7edf\u3001\u7f13\u5b58\u548c\u6ce2\u52a8\u4fdd\u7559 20%\u201325%\uff0c256 GB \u7ea7\u5185\u5b58\u6bd4\u628a 192 GB \u521a\u597d\u5206\u6ee1\u66f4\u5408\u7406\u3002\u82e5\u53ea\u6709 128 GB\uff0c\u5c31\u5e94\u8be5\u6392\u961f\u4e32\u884c\uff0c\u800c\u4e0d\u662f\u8ba9\u4e24\u4e2a\u4efb\u52a1\u4e92\u76f8\u62a2\u5185\u5b58\u3002<\/p>\n

\u5e76\u53d1\u89c4\u5212\u8fd8\u8981\u770b\u5171\u4eab\u76d8\u3002\u56db\u4e2a\u4efb\u52a1\u540c\u65f6\u8bfb\u53d6 FASTQ\u3001\u5199\u5165\u4e2d\u95f4\u6587\u4ef6\uff0c\u5373\u4f7f\u5185\u5b58\u591f\uff0c\u4e5f\u53ef\u80fd\u628a\u78c1\u76d8\u541e\u5410\u6253\u6ee1\uff0c\u4f7f\u6bcf\u4e2a\u4efb\u52a1\u90fd\u53d8\u6162\u3002\u66f4\u7a33\u59a5\u7684\u505a\u6cd5\u662f\u5148\u6d4b\u4e00\u4e2a\u4efb\u52a1\uff0c\u518d\u9010\u6b65\u589e\u52a0\u5230\u4e24\u4e2a\uff0c\u6bd4\u8f83\u603b\u541e\u5410\u3001\u7b49\u5f85\u65f6\u95f4\u548c\u5931\u8d25\u7387\uff1b\u53ea\u6709\u6574\u4f53\u6548\u7387\u63d0\u9ad8\uff0c\u589e\u52a0\u5e76\u53d1\u624d\u6709\u610f\u4e49\u3002\u56e2\u961f\u591a\u4eba\u5171\u7528\u8282\u70b9\u65f6\uff0c\u8fd8\u5e94\u7ed9\u6bcf\u4e2a\u4efb\u52a1\u8bbe\u7f6e\u8d44\u6e90\u4e0a\u9650\u548c\u72ec\u7acb\u76ee\u5f55\u3002<\/p>\n

\u6838\u5fc3\u6570\u589e\u52a0\u4e5f\u4e0d\u4e00\u5b9a\u7ebf\u6027\u7f29\u77ed\u65f6\u95f4\u3002Space Ranger \u4f1a\u4e3a\u6bcf\u4e2a\u6838\u5fc3\u6d3e\u751f\u591a\u4e2a\u8fdb\u7a0b\uff1b\u6838\u5fc3\u8d8a\u591a\uff0c\u8fdb\u7a0b\u6570\u548c\u6587\u4ef6\u53e5\u67c4\u538b\u529b\u4e5f\u4f1a\u4e0a\u5347\u3002\u770b\u5230\u201cCPU \u6ca1\u8dd1\u6ee1\u201d\u65f6\uff0c\u5148\u770b I\/O\u3001\u5185\u5b58\u548c\u6587\u4ef6\u9650\u5236\uff0c\u4e0d\u8981\u53ea\u7ee7\u7eed\u52a0\u7ebf\u7a0b\u3002<\/p>\n

\u8fd0\u884c\u4e2d\u4e0d\u8981\u53ea\u76ef\u7740\u8fdb\u5ea6\u6761<\/h2>\n

\u81f3\u5c11\u540c\u65f6\u8bb0\u5f55\u56db\u7c7b\u6307\u6807\uff1a\u8fdb\u7a0b\u5cf0\u503c\u5185\u5b58\u3001CPU \u5229\u7528\u7387\u3001\u78c1\u76d8 iowait<\/code> \u548c\u5de5\u4f5c\u76ee\u5f55\u5269\u4f59\u7a7a\u95f4\u3002\u5cf0\u503c\u5185\u5b58\u6301\u7eed\u8d34\u8fd1\u4e0a\u9650\uff0c\u8bf4\u660e\u4e0b\u4e00\u6b21\u66f4\u5927\u6837\u672c\u5bb9\u6613\u88ab\u7cfb\u7edf\u7ec8\u6b62\uff1bCPU \u5229\u7528\u7387\u4e0d\u9ad8\u4f46 iowait<\/code> \u957f\u65f6\u95f4\u5347\u9ad8\uff0c\u901a\u5e38\u5e94\u5148\u68c0\u67e5\u78c1\u76d8\u548c\u5171\u4eab\u5b58\u50a8\uff1b\u78c1\u76d8\u5269\u4f59\u7a7a\u95f4\u5feb\u901f\u4e0b\u964d\uff0c\u5219\u8981\u5224\u65ad\u589e\u957f\u6765\u81ea\u4e34\u65f6\u6587\u4ef6\u3001BAM \u8fd8\u662f\u6700\u7ec8\u8f93\u51fa\u3002<\/p>\n

\u53ef\u4ee5\u7528 \/usr\/bin\/time -v<\/code> \u8bb0\u5f55\u5355\u4efb\u52a1\u6700\u5927\u5e38\u9a7b\u5185\u5b58\uff0c\u7528 free -h<\/code> \u548c df -h<\/code> \u770b\u5185\u5b58\u3001\u4ea4\u6362\u7a7a\u95f4\u548c\u78c1\u76d8\u4f59\u91cf\uff0c\u7528 iostat -x<\/code> \u89c2\u5bdf\u8bbe\u5907\u7b49\u5f85\u3002\u6bcf\u6b21\u4fdd\u7559\u547d\u4ee4\u3001\u7248\u672c\u3001\u65e5\u5fd7\u548c\u8d44\u6e90\u8bb0\u5f55\uff0c\u4e0b\u4e00\u6279\u6837\u672c\u624d\u80fd\u6309\u5b9e\u6d4b\u6392\u961f\u3002<\/p>\n

spaceranger count --id=sample01 \\\n  --fastqs=\/data\/fastq \\\n  --transcriptome=\/refs\/GRCh38 \\\n  --localcores=32 --localmem=128<\/code><\/pre>\n
\u5177\u4f53\u8f93\u5165\u53c2\u6570\u8981\u6309\u5b9e\u9a8c\u7c7b\u578b\u548c Space Ranger \u7248\u672c\u8c03\u6574\u3002\u82e5\u4e0b\u6e38\u660e\u786e\u4e0d\u9700\u8981 BAM\uff0c\u53ef\u8bc4\u4f30 --create-bam=false<\/code> \u662f\u5426\u9002\u7528\uff1b\u8fd9\u80fd\u51cf\u5c11\u90e8\u5206\u8f93\u51fa\uff0c\u4f46\u4e0d\u80fd\u628a\u5b83\u5f53\u6210\u6240\u6709\u9879\u76ee\u7684\u9ed8\u8ba4\u9009\u9879\u3002<\/p>\n
\u4e0a\u673a\u524d\u5148\u505a\u8fd9 5 \u9879\u68c0\u67e5<\/h2>\n
    \n
  1. \u9501\u5b9a\u7248\u672c\u4e0e\u8f93\u5165\u3002<\/strong>\u8bb0\u5f55\u7248\u672c\u3001FASTQ \u603b\u91cf\u3001\u53c2\u8003\u6216 probe set\u3001\u56fe\u50cf\u683c\u5f0f\u548c\u50cf\u7d20\u5c3a\u5bf8\u3002<\/li>\n
  2. \u5148\u8dd1\u4ee3\u8868\u6027\u6837\u672c\u3002<\/strong>\u9009\u62e9 reads \u8f83\u591a\u3001\u56fe\u50cf\u8f83\u5927\u7684\u6837\u672c\uff0c\u8bb0\u5f55\u5cf0\u503c\u5185\u5b58\u3001\u65f6\u95f4\u548c\u76ee\u5f55\u589e\u957f\u3002<\/li>\n
  3. \u660e\u786e\u9650\u5236\u8d44\u6e90\u3002<\/strong>\u7528 --localcores<\/code>\u3001--localmem<\/code> \u63a7\u5236\u5355\u4efb\u52a1\u4e0a\u9650\u3002<\/li>\n
  4. \u628a\u5b58\u50a8\u5f53\u4f5c\u6d41\u7a0b\u8d44\u6e90\u3002<\/strong>\u628a\u539f\u59cb\u6570\u636e\u3001\u4e34\u65f6\u6587\u4ef6\u3001\u6700\u7ec8\u7ed3\u679c\u548c\u5907\u4efd\u4e00\u8d77\u8ba1\u7b97\u3002<\/li>\n
  5. \u518d\u51b3\u5b9a\u5e76\u53d1\u3002<\/strong>\u7528\u201c\u5355\u4efb\u52a1\u5cf0\u503c \u00d7 \u5e76\u53d1\u6570 + \u7cfb\u7edf\u4f59\u91cf\u201d\u4f30\u7b97\u5185\u5b58\u3002<\/li>\n<\/ol>\n
    \u5982\u679c\u4f7f\u7528\u8d85\u5927\u5207\u7247\uff0c\u56fe\u50cf\u672c\u8eab\u4e5f\u4e0d\u80fd\u5ffd\u7565\u300210x \u7684\u6210\u50cf\u8bf4\u660e\u6307\u51fa\uff0c\u76f8\u5173\u56fe\u50cf\u53ef\u8fbe\u5230 1\u2013100 GB\uff1b64 GB \u5185\u5b58\u5bf9\u5e94\u7684\u56fe\u50cf\u5904\u7406\u4e0a\u9650\u793a\u4f8b\u7ea6\u4e3a 4.5 gigapixels\uff0c\u4e5f\u5c31\u662f\u7ea6 67,000 \u00d7 67,000 \u50cf\u7d20\u3002\u538b\u7f29\u6587\u4ef6\u770b\u8d77\u6765\u4e0d\u5927\uff0c\u89e3\u7801\u548c\u5904\u7406\u65f6\u7684\u5185\u5b58\u5360\u7528\u4ecd\u53ef\u80fd\u660e\u663e\u4e0a\u5347\u3002<\/p>\n
    \u4ec0\u4e48\u65f6\u5019\u66f4\u9002\u5408\u653e\u5230\u670d\u52a1\u5668\u4e0a\uff1f<\/h2>\n
    \u5f53\u9879\u76ee\u6ee1\u8db3\u4efb\u610f\u4e24\u9879\u2014\u2014Visium HD\u3001\u5927\u56fe\u3001\u591a\u6837\u672c\u3001\u9700\u8981\u5e76\u884c\u3001\u56e2\u961f\u534f\u4f5c\u3001\u540e\u7eed\u8fd8\u8981\u505a\u5206\u5272\u6216\u6df1\u5ea6\u5b66\u4e60\u2014\u2014\u670d\u52a1\u5668\u901a\u5e38\u6bd4\u4e2a\u4eba\u7535\u8111\u66f4\u5408\u9002\u3002\u4ef7\u503c\u4e0d\u53ea\u662f\u201c\u914d\u7f6e\u66f4\u9ad8\u201d\uff0c\u8fd8\u5305\u62ec\u56fa\u5b9a\u8f6f\u4ef6\u7248\u672c\u3001\u96c6\u4e2d\u5b58\u50a8\u3001\u4efb\u52a1\u6392\u961f\u3001\u65e5\u5fd7\u4fdd\u7559\u548c\u590d\u73b0\u5b9e\u9a8c\u73af\u5883\u3002<\/p>\n
    \u4f46\u670d\u52a1\u5668\u79df\u7528\u3001\u73af\u5883\u90e8\u7f72\u548c\u59d4\u6258\u5206\u6790\u662f\u4e09\u79cd\u4e0d\u540c\u670d\u52a1\u3002\u79df\u7528\u73af\u5883\u4e0d\u7b49\u4e8e\u81ea\u52a8\u5305\u542b\u5206\u6790\u4ea4\u4ed8\uff1b\u59d4\u6258\u5206\u6790\u4e5f\u8981\u5148\u786e\u8ba4\u6570\u636e\u3001\u76ee\u6807\u548c\u7ed3\u679c\u8303\u56f4\u3002<\/p>\n
    \n
    \u628a\u8d44\u6e90\u95ee\u9898\u63d0\u524d\u7b97\u6e05\u695a<\/h2>\n
    \u5982\u679c Space Ranger \u5728\u6bd4\u5bf9\u3001\u56fe\u50cf\u5904\u7406\u6216\u77e9\u9635\u751f\u6210\u9636\u6bb5\u4e2d\u65ad\uff0c\u53ef\u4ee5\u5148\u51c6\u5907\uff1a\u8f6f\u4ef6\u7248\u672c\u3001\u6837\u672c\u6570\u3001FASTQ \u603b\u91cf\u3001\u56fe\u50cf\u5c3a\u5bf8\u4e0e\u683c\u5f0f\u3001\u5f53\u524d\u673a\u5668\u914d\u7f6e\u3001\u62a5\u9519\u9636\u6bb5\u548c\u5e0c\u671b\u5b8c\u6210\u7684\u65f6\u95f4<\/strong>\u3002\u4e91\u751f\u4fe1\u4f1a\u5148\u5224\u65ad\u74f6\u9888\u5c5e\u4e8e\u5185\u5b58\u3001\u5b58\u50a8\u3001I\/O\u3001\u73af\u5883\u8fd8\u662f\u5e76\u53d1\u7b56\u7565\uff0c\u518d\u6c9f\u901a\u9002\u5408\u7684\u670d\u52a1\u5668\u73af\u5883\u3001\u90e8\u7f72\u652f\u6301\u6216\u5206\u6790\u670d\u52a1\u8303\u56f4\u3002<\/p>\n
        \u8054\u7cfb\u4e91\u751f\u4fe1\uff0c\u54a8\u8be2\u7a7a\u95f4\u8f6c\u5f55\u7ec4\u7b97\u529b\u4e0e\u73af\u5883<\/a>\n  <\/div>\n
    \u53c2\u8003\u8d44\u6599<\/h2>\n