{"id":61713,"date":"2024-11-19T15:32:33","date_gmt":"2024-11-19T07:32:33","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61713"},"modified":"2024-11-19T15:32:33","modified_gmt":"2024-11-19T07:32:33","slug":"sra%e6%96%87%e4%bb%b6%e8%bf%98%e8%83%bd%e8%bf%99%e4%b9%88%e5%a4%84%e7%90%86%ef%bc%9f%e4%b8%8b%e8%bd%bd%e8%b6%85%e7%ba%a7%e5%bf%ab%e7%9a%84ascp%e5%92%8c%e8%b6%85%e7%ba%a7%e7%ae%80%e5%8d%95%e7%9a%84","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=61713","title":{"rendered":"sra\u6587\u4ef6\u8fd8\u80fd\u8fd9\u4e48\u5904\u7406\uff1f\u4e0b\u8f7d\u8d85\u7ea7\u5feb\u7684ascp\u548c\u8d85\u7ea7\u7b80\u5355\u7684\u8ba1\u6570\u5de5\u5177salmon\u5e26\u4f60\u4f53\u9a8c\u98de\u4e00\u822c\u7684\u611f\u89c9"},"content":{"rendered":"\n

\u5927\u5bb6\u597d\u554a\uff0c\u5728\u516c\u5171\u6570\u636e\u5e93\u4e2d\u6211\u4eec\u8fd8\u7ecf\u5e38\u4f1a\u9047\u5230\u8f6c\u5f55\u7ec4\u6570\u636e\uff0c\u8f6c\u5f55\u7ec4\u6570\u636e\u662f\u65e0\u6cd5\u7528R\u5305\u4e0b\u8f7d\u7684\uff0c\u56e0\u4e3a\u8f6c\u5f55\u7ec4\u6570\u636e\u7684Series Matrix File(s)<\/a>\u6ca1\u6709\u57fa\u56e0\u8868\u8fbe\u91cf\u6570\u636e\uff0c\u53ea\u6709\u4e34\u5e8a\u6570\u636e\uff0c\u6240\u4ee5\u6bcf\u6b21\u5904\u7406\u8f6c\u5f55\u7ec4\u6570\u636e\u6211\u4eec\u90fd\u8981\u5728Supplementary file\u4e0b\u8f7d\u6587\u4ef6\u7136\u540e\u5904\u7406\uff0c\u4f46\u662f\u5f88\u4e0d\u5de7\u7684\u662f\u5f88\u5c11\u6709\u4f5c\u8005\u4f1a\u4e0a\u4f20\u4ed6\u4eec\u6574\u5408\u597d\u7684\u6570\u636e\uff0c\u5927\u90e8\u5206\u4f5c\u8005\u90fd\u4f1a\u4e0a\u4f20\u672a\u6574\u5408\u7684\u6570\u636e\uff0c\u8fd9\u65f6\u5019\u6211\u4eec\u9700\u8981\u4ece\u5934\u5f00\u59cb\u6574\u5408\u6570\u636e\u3002<\/p>\n\n\n\n

\u4ece\u5934\u5f00\u59cb\u6574\u5408\u6570\u636e\u5df2\u7ecf\u5f88\u9ebb\u70e6\u4e86\uff0c\u6709\u7684\u4f5c\u8005\u751a\u81f3\u4e0a\u4f20\u7684\u4e0d\u662f\u672a\u6574\u5408\u7684\u8868\u8fbe\u91cf\u6570\u636e\uff0c\u6bd4\u5982GSE104140\u548cGSE58150\uff0c\u4ed6\u4eec\u4e0a\u4f20bw\u6216wig\u6587\u4ef6\uff0c\u4ee4\u4eba\u7a92\u606f\uff0c\u867d\u7136\u6709\u6587\u732e\u63d0\u5230\u53ef\u4ee5\u7528bw\u6587\u4ef6\u6765\u5b58\u50a8RNA-seq\u6570\u636e\uff0c\u4f46\u662f\u5c0f\u82b1\u6ca1\u6709\u627e\u5230\u5982\u4f55\u624d\u80fd\u5c06bw\u6587\u4ef6\u8f6c\u4e3a\u57fa\u56e0\u8868\u8fbe\u91cf\u6587\u4ef6\u3002\u6240\u4ee5\u8fd9\u65f6\u5019\u6211\u4eec\u9700\u8981\u4e0b\u8f7d\u6700\u539f\u59cb\u7684fastq\u6587\u4ef6\u6765\u4ece\u5934\u5f00\u59cb\u5904\u7406\uff0c\u542c\u5230\u8fd9\u91cc\u4e5f\u8bb8\u4f60\u5df2\u7ecf\u5f00\u59cb\u5934\u5927\u4e86\uff0c\u4f46\u662f\u4e0d\u8981\u614c\uff0c\u5c0f\u82b1\u624b\u628a\u624b\u6559\u4f60\u5982\u4f55\u4ece\u6570\u636e\u4e0b\u8f7d\u5230\u6570\u636e\u5904\u7406\u5230\u5f97\u5230\u7ed3\u679c\uff0c\u5e26\u4f60\u4f53\u9a8c\u98de\u4e00\u822c\u7684\u611f\u89c9\u3002\u8981\u662f<\/strong>\u60a8<\/strong>\u6709\u81ea\u5df1\u505a\u4e0d\u4e86\u7684\u751f\u4fe1\u5206\u6790\uff0c\u53ef\u4ee5\u8054\u7cfb<\/strong>\u6211\u3002\u8981\u8fdb\u884c\u4e0b\u9762\u7684\u64cd\u4f5c\u60a8\u8fd8\u9700\u8981\u4e00\u4e2a\u670d\u52a1\u5668\uff0c\u6b22\u8fce\u8054\u7cfb\u5c0f\u82b1\u79df\u8d41\u9ad8\u6027\u4ef7\u6bd4\u7684\u670d\u52a1\u5668\u54e6<\/strong>\u3002<\/strong><\/strong><\/p>\n\n\n\n

\u7136\u540e\u6211\u4eec\u5f00\u59cb\u51c6\u5907\u4e0b\u8f7d\u6570\u636e\u5427\uff0c\u4e00\u822c\u7684\u65b9\u6cd5\u5c31\u662f\u4f7f\u7528sra-toolkit\u7684prefetch\u6765\u4e0b\u8f7d\u6570\u636e\u3002\u4ee5GSE58150\u4e3a\u4f8b\uff0c\u9996\u5148\u5728NCBI\u7684GEO\u6570\u636e\u5e93\u641c\u7d22GSE58150\uff0c\u7136\u540e\u5728\u6700\u4e0b\u9762\u627e\u5230SRA Run Selector<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u7136\u540e\u6311\u9009\u4f60\u60f3\u8981\u7684\u6837\u672c\u6216\u662f\u9009\u62e9\u6240\u6709\u6837\u672c\uff0c\u4e0b\u8f7dAccession List\uff0c<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u6587\u4ef6\u4e0b\u8f7d\u4e0b\u6765\u662f\u8fd9\u4e2a\u6837\u5b50\u7684\uff0c\u91cc\u9762\u662f\u60a8\u9009\u62e9\u7684\u6837\u672c\u7684SRR\u53f7<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u7136\u540e\u5728\u670d\u52a1\u5668\u4e0a\u8fd0\u884c\u547d\u4ee4\uff1aprefetch –option-file GSE58150_Acc_List.txt\u8fd9\u6837\u53ef\u4ee5\u6279\u91cf\u4e0b\u8f7d\u6570\u636e\u3002<\/p>\n\n\n\n

\u8fd9\u6837\u65b9\u4fbf\u662f\u65b9\u4fbf\uff0c\u4f46\u662f\u901f\u5ea6\u592a\u6162\u4e86\uff0c\u4e00\u5bf8\u5149\u9634\u4e00\u5bf8\u91d1\uff0c\u7279\u522b\u662f\u5bf9\u4e8e\u79d1\u7814\u5de5\u4f5c\u8005\u3002\u8fd9\u65f6\u5019\u5927\u5bb6\u53ef\u4ee5\u7528ascp\u6765\u4e0b\u8f7d\u6570\u636e\uff0c\u4e0b\u9762\u5c0f\u82b1\u5c31\u6559\u5927\u5bb6\u5982\u4f55\u4f7f\u7528ascp\u6765\u4e0b\u8f7d\u6570\u636e\u3002<\/p>\n\n\n\n

\u9996\u5148\u6211\u4eec\u9700\u8981\u8fd9\u4e2aBioProject<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u7136\u540e\u53bbENA\u6570\u636e\u5e93\u641c\u7d22\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n
\"\"<\/figure>\n\n\n\n

\u8fd9\u6837\u5c31\u590d\u5236\u4e0b\u6765\u6211\u4eec\u7684\u76ee\u6807\u4e0b\u8f7d\u5730\u5740\u4e86\uff1aera-fasp@fasp.sra.ebi.ac.uk:\/vol1\/srr\/SRR131\/001\/SRR1313291<\/p>\n\n\n\n

\u7136\u540e\u4f7f\u7528\u547d\u4ee4\uff1a<\/p>\n\n\n\n

ascp -P 33001 -k 1 -l 200m -T -i ~\/.aspera\/connect\/etc\/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:\/vol1\/srr\/SRR131\/001\/SRR1313291 .\/<\/p>\n\n\n\n

\u8fd9\u91cc\u5efa\u8bae\u628a\u6240\u6709\u4e0b\u8f7d\u5730\u5740\u90fd\u6574\u7406\u5230\u4e00\u4e2a\u6587\u4ef6\u4e2d\uff0c\u6bd4\u5982\u8fd9\u6837\uff1a<\/p>\n\n\n\n

\"\"<\/figure>\n\n\n\n

\u7136\u540e\u7528for\u5faa\u73af\u6765\u9010\u4e2a\u8bfb\u53d6\u4e0b\u8f7d\uff0c\u4f46\u662f\u6709\u65f6\u5019ascp\u4f1a\u6709\u4e0b\u8f7d\u5931\u8d25\u7684\u60c5\u51b5\uff0c\u8fd9\u65f6\u5019\u5c31\u9700\u8981\u91cd\u65b0\u4e0b\u8f7d\u3002\u542c\u4e0a\u53bb\u662f\u4e0d\u662f\u5f88\u9ebb\u70e6\u4f60\uff0c\u522b\u62c5\u5fc3\uff0c\u5c0f\u82b1\u5df2\u7ecf\u5199\u597d\u4e86\u81ea\u52a8\u4e0b\u8f7d\u548c\u81ea\u52a8\u91cd\u65b0\u4e0b\u8f7d\u7684\u4ee3\u7801\uff1a<\/p>\n\n\n\n

GSE_id = “GSE58150”<\/p>\n\n\n\n

url = read.table(paste0(“.\/”, GSE_id, “_access.txt”), header = TRUE)<\/p>\n\n\n\n

for(i in 1:nrow(url)){<\/p>\n\n\n\n

system(paste0(“ascp -P 33001 -k 1 -l 200m -T -i ~\/.aspera\/connect\/etc\/asperaweb_id_dsa.openssh “,<\/p>\n\n\n\n

url[i, 2], ” .\/raw_data\/”, GSE_id, “\/”))<\/p>\n\n\n\n

}<\/p>\n\n\n\n

exist_file = list.files(paste0(“.\/raw_data\/”, GSE_id, “\/”))<\/p>\n\n\n\n

fail_file = which(!url$run_id %in% exist_file)<\/p>\n\n\n\n

while(length(fail_file!=0)){<\/p>\n\n\n\n

for(i in fail_file){<\/p>\n\n\n\n

system(paste0(“ascp -P 33001 -k 1 -l 200m -T -i ~\/.aspera\/connect\/etc\/asperaweb_id_dsa.openssh “,<\/p>\n\n\n\n

url[i, 2], ” .\/raw_data\/”, GSE_id, “\/”))<\/p>\n\n\n\n

}<\/p>\n\n\n\n

exist_file = list.files(paste0(“.\/raw_data\/”, GSE_id, “\/”))<\/p>\n\n\n\n

fail_file = which(!url$run_id %in% exist_file)<\/p>\n\n\n\n

}<\/p>\n\n\n\n

\u628a\u6587\u4ef6\u4e0b\u8f7d\u4e0b\u6765\u4e4b\u540e\u8fd8\u8981\u8fdb\u884c\u5904\u7406\uff0c\u522b\u62c5\u5fc3\uff0c\u8fd9\u91cc\u5c0f\u82b1\u4e5f\u6574\u7406\u597d\u4e86\u6d41\u7a0b\u5316\u7684\u4ee3\u7801\uff0c\u60a8\u53ea\u9700\u8981\u521b\u5efa\u51e0\u4e2a\u6587\u4ef6\u5939\u7136\u540e\u8bbe\u7f6e\u51e0\u4e2a\u8def\u5f84\u5c31\u53ef\u4ee5\u8fdb\u884c\u5b8c\u6240\u6709\u6d41\u7a0b\uff1a<\/p>\n\n\n\n

samples = list.files(paste0(“.\/raw_data\/”, GSE_id))<\/p>\n\n\n\n

fastq_dir = paste0(“\/media\/desk16\/iyunwf\/ascp_down_test\/”)<\/p>\n\n\n\n

fastp_dir = paste0(“.\/fastp_data\/”)<\/p>\n\n\n\n

salmon_dir = paste0(“.\/salmon_result\/”)<\/p>\n\n\n\n

sra_dir = paste0(“.\/raw_data\/”, GSE_id, “\/”)<\/p>\n\n\n\n

salmon_index = “.\/ref\/GRCh38_salmon_index”<\/p>\n\n\n\n

for(i in 1:20){<\/p>\n\n\n\n

sra_file = paste0(sra_dir, “\/”, samples[i])<\/p>\n\n\n\n

system(paste0(“fastq-dump –gzip –split-3 –defline-qual ‘+’ –defline-seq ‘@\\\\$ac-\\\\$si\/\\\\$ri’ “, sra_file, ” -O “, fastq_dir))<\/p>\n\n\n\n

system(paste0(“rm “, sra_file))<\/p>\n\n\n\n

system(paste0(“fastp -i “, fastq_dir, “\/”, samples[i], “_1.fastq.gz “, “-I “, fastq_dir, “\/”, samples[i], “_2.fastq.gz “,<\/p>\n\n\n\n

“-o “, fastp_dir, “\/”, samples[i], “.R1.fq.gz -O “, fastp_dir, “\/”, samples[i], “.R2.fq.gz “,<\/p>\n\n\n\n

“–thread 5”))<\/p>\n\n\n\n

system(paste0(“rm “, fastq_dir, “\/”, samples[i], “_1.fastq.gz “, fastq_dir, “\/”, samples[i], “_2.fastq.gz”))<\/p>\n\n\n\n

system(paste0(“salmon quant -i “, salmon_index, ” -l A “,<\/p>\n\n\n\n

“-1 “, fastp_dir, “\/”, samples[i], “.R1.fq.gz -2 “, fastp_dir, “\/”, samples[i], “.R2.fq.gz “,<\/p>\n\n\n\n

“-p 8 –validateMappings -o “, salmon_dir, “\/”, GSE_id, “\/”, samples[i], “_quant”))<\/p>\n\n\n\n

system(paste0(“rm “, fastp_dir, “\/”, samples[i], “.R1.fq.gz “, fastp_dir, “\/”, samples[i], “.R2.fq.gz”))<\/p>\n\n\n\n

}<\/p>\n\n\n\n

\u628a\u6570\u636e\u5904\u7406\u5b8c\u4e4b\u540e\u6211\u4eec\u8fd8\u8981\u628a\u6570\u636e\u6574\u5408\u4e00\u4e0b\uff0c\u8fd9\u91cc\u4e5f\u53ef\u4ee5\u7528\u5c0f\u82b1\u7684\u4ee3\u7801\u4e00\u6b21\u5b8c\u6210\uff1a<\/p>\n\n\n\n

GSE_id = “GSE58150”<\/p>\n\n\n\n

salmon_dir = paste0(“.\/salmon_result\/”, GSE_id, “\/”)<\/p>\n\n\n\n

samples = list.files(salmon_dir)<\/p>\n\n\n\n

library(stringr)<\/p>\n\n\n\n

samples = str_extract(samples, “(.*?)_quant”, group = 1)<\/p>\n\n\n\n

files = paste0(salmon_dir, “\/”, samples, “_quant\/quant.sf”)<\/p>\n\n\n\n

for(i in 1:length(files)){<\/p>\n\n\n\n

tmp = read.table(files[i], header = TRUE)<\/p>\n\n\n\n

tmp = tmp[,c(1, 5)]<\/p>\n\n\n\n

rownames(tmp) = tmp[,1]<\/p>\n\n\n\n

colnames(tmp)[2] = samples[i]<\/p>\n\n\n\n

if(i == 1){<\/p>\n\n\n\n

merged_data = tmp<\/p>\n\n\n\n

}else{<\/p>\n\n\n\n

merged_data = cbind(merged_data, tmp[,2, drop = FALSE])<\/p>\n\n\n\n

}<\/p>\n\n\n\n

}<\/p>\n\n\n\n

merged_data$ENST_id = str_extract(merged_data$Name, “(.*?)\\\\.”, group = 1)<\/p>\n\n\n\n

write.csv(merged_data, paste0(“.\/data\/data_”, GSE_id, “.csv”))<\/p>\n\n\n\n

\u63a5\u4e0b\u6765\u5c31\u662f\u6b63\u5e38\u7684\u57fa\u56e0\u6ce8\u91ca\uff0c\u91cd\u590d\u57fa\u56e0\u53d6\u5747\u503c\u7684\u6b65\u9aa4\u4e86\u3002\u76f8\u4fe1\u5927\u5bb6\u5df2\u7ecf\u505a\u7684\u5f88\u719f\u7ec3\u4e86\u3002<\/p>\n\n\n\n

\u505a\u6570\u636e\u6316\u6398\u4e00\u5b9a\u8981\u719f\u6089\u5404\u4e2a\u6570\u636e\u5e93\u7684\u4f7f\u7528\uff0c\u800c\u4e14\u8981\u719f\u6089\u6570\u636e\u5e93\u91cc\u5404\u79cd\u6570\u636e\u7c7b\u578b\uff0c\u9664\u4e86\u8981\u6709\u8fc7\u786c\u7684\u57fa\u7840\u77e5\u8bc6\uff0c\u4e00\u4e2a\u597d\u7684\u5de5\u5177\u4e5f\u662f\u5fc5\u4e0d\u53ef\u5c11\u7684\uff0c\u5de5\u6b32\u5584\u5176\u4e8b\u5fc5\u5148\u5229\u5176\u5668\uff0c\u8981\u505a\u8fd9\u4e9b\u64cd\u4f5c\uff0c\u4f60\u8981\u6709\u4e00\u4e2a\u670d\u52a1\u5668\uff0c\u7a7a\u95f4\u591f\u5927\uff0c\u5185\u5b58\u591f\u5927\uff0c\u7ebf\u7a0b\u591f\u591a\uff0c\u6b22\u8fce\u5927\u5bb6\u8054\u7cfb\u5c0f\u82b1\u79df\u8d41\u9ad8\u6027\u4ef7\u6bd4\u7684\u670d\u52a1\u5668\u54e6<\/strong>\u3002<\/strong>\u597d\u4e86\uff0c\u4eca\u5929\u7684\u77e5\u8bc6\u5c31\u5206\u4eab\u5230\u8fd9\u91cc\u4e86\uff0c\u5e0c\u671b\u5bf9\u5927\u5bb6\u80fd\u6709\u6240\u5e2e\u52a9\uff0c\u5982\u679c\u5927\u5bb6\u6709\u5176\u4ed6\u7591\u95ee\u6216\u8005\u53d1\u73b0\u6587\u4e2d\u6709\u4e0d\u5bf9\u7684\u5730\u65b9\uff0c\u6b22\u8fce\u7559\u8a00\u5206\u4eab\u3002\u5982\u679c\u5404\u4f4d\u89c9\u5f97\u81ea\u5df1\u8fd0\u884c\u4ee3\u7801\u592a\u9ebb\u70e6\uff0c\u6b22\u8fce\u7528\u6211\u4eec\u7684\u4e91\u751f\u4fe1\u5c0f\u5de5\u5177<\/strong>(<\/strong>http:\/\/www.biocloudservice.com\/home.html<\/strong>)<\/strong>\uff0c\u53ea\u8981\u8f93\u5165\u5408\u9002\u7684\u6570\u636e\u5c31\u53ef\u4ee5\u76f4\u63a5\u51fa\u60f3\u8981\u7684\u56fe\u5462<\/strong>\u3002<\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

\u5927\u5bb6\u597d\u554a\uff0c\u5728\u516c\u5171\u6570\u636e\u5e93\u4e2d\u6211\u4eec\u8fd8\u7ecf\u5e38\u4f1a\u9047\u5230\u8f6c\u5f55\u7ec4\u6570\u636e\uff0c\u8f6c\u5f55\u7ec4\u6570\u636e\u662f\u65e0\u6cd5\u7528R\u5305\u4e0b\u8f7d\u7684\uff0c\u56e0\u4e3a\u8f6c\u5f55\u7ec4\u6570\u636e\u7684Series […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"","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\/61713"}],"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=61713"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61713\/revisions"}],"predecessor-version":[{"id":61722,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/61713\/revisions\/61722"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=61713"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=61713"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=61713"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}