{"id":24856,"date":"2024-01-17T10:36:16","date_gmt":"2024-01-17T02:36:16","guid":{"rendered":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24856"},"modified":"2024-01-17T10:36:19","modified_gmt":"2024-01-17T02:36:19","slug":"%e5%b0%8f%e6%9e%9c%e4%b8%89%e5%88%86%e9%92%9f%e6%95%99%e4%bc%9a%e4%bd%a0%e5%a6%82%e4%bd%95%e4%bd%bf%e7%94%a8trinity%e5%81%9a%e8%bd%ac%e5%bd%95%e6%9c%ac%e7%bb%84%e8%a3%85%ef%bc%88%e4%b8%8a%ef%bc%89","status":"publish","type":"post","link":"http:\/\/www.biocloudservice.com\/wordpress\/?p=24856","title":{"rendered":"\u5c0f\u679c\u4e09\u5206\u949f\u6559\u4f1a\u4f60\u5982\u4f55\u4f7f\u7528Trinity\u505a\u8f6c\u5f55\u672c\u7ec4\u88c5\uff08\u4e0a\uff09"},"content":{"rendered":"<p>Trinity, \u662f\u7531Broad Institute\u5f00\u53d1\u7684\u8fdb\u884cde novo\u8f6c\u5f55\u672c\u7ec4\u88c5\u7684\u5de5\u5177\uff0c\u5b83\u80fd\u5c06RNA-seq reads\u62fc\u63a5\u6210\u66f4\u957f\u7684\u8f6c\u5f55\u672c\u3002Trinity\u7531\u4e09\u4e2a\u6a21\u5757\u7ec4\u6210\uff0c\u5176\u57fa\u672c\u4f5c\u7528\u5982\u4e0b\u6240\u793a\uff1a<\/p>\n<ul>\n<li><em>Inchworm<\/em>\uff1a\u5c06RNA-seq reads\u7ec4\u88c5\u6210\u5355\u4e2a\u8f6c\u5f55\u672c<\/li>\n<li><em>Chrysails<\/em>\uff1a\u5c06\u4e0a\u4e00\u6b65\u5f62\u6210\u7684\u8f6c\u5f55\u672c\u8fdb\u884c\u805a\u7c7b\uff0c\u5bf9\u4e8e\u6bcf\u4e00\u4e2a\u805a\u7c7b\u5f62\u6210\u5b8c\u6574\u7684de Bruijin graphs\u3002\u6bcf\u4e00\u4e2a\u805a\u7c7b\u4ee3\u8868\u4e00\u4e2a\u57fa\u4e8e\u8f6c\u5f55\u672c\u7684\u590d\u6742\u7a0b\u5ea6\u3002<\/li>\n<li><em>Butterfly<\/em>\uff1a\u5e76\u884c\u7684\u5904\u7406\u6bcf\u4e00\u4e2a\u56fe\uff0c\u8ffd\u8e2a\u56fe\u4e2dreads\u548c\u914d\u5bf9reads\u7684\u8def\u5f84\uff0c\u6700\u540e\u62a5\u9053\u53ef\u53d8\u526a\u5207\u4e9a\u578b\u7684\u5168\u957f\u8f6c\u5f55\u672c\u3002<\/li>\n<\/ul>\n<p>\u5feb\u6765\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u5b66\u4e60\u5427\uff01<\/p>\n<ol>\n<li><strong>\u8f6f\u4ef6\u5b89\u88c5<\/strong><\/li>\n<\/ol>\n<p>Trinity\u9700\u8981\u5728Linux\u7cfb\u7edf\u4e0a\u8fd0\u884c\u3002<\/p>\n<p>\u8f6f\u4ef6\u4e0b\u8f7d\u94fe\u63a5\uff1a<a href=\"https:\/\/github.com\/trinityrnaseq\/trinityrnaseq\/releases\">https:\/\/github.com\/trinityrnaseq\/trinityrnaseq\/releases<\/a> <img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"400\" class=\"wp-image-24857\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-1.png?resize=640%2C400\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-1.png?w=1709 1709w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-1.png?resize=300%2C188 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-1.png?resize=1024%2C641 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-1.png?resize=768%2C480 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-1.png?resize=1536%2C961 1536w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-1.png?resize=600%2C375 600w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-1.png?w=1280 1280w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u6211\u4eec\u6253\u5f00\u53ef\u4ee5\u53d1\u73b0\u8be5\u8f6f\u4ef6\u5f00\u53d1\u7684\u5f88\u65e9\uff0c\u4f46\u4ecd\u7136\u80fd\u4fdd\u6301\u6bcf\u5e74\u66f4\u65b0\u7684\u72b6\u6001\uff0c\u662f\u975e\u5e38\u96be\u5f97\u7684\uff01\u6211\u4eec\u9009\u62e9\u6700\u65b0\u7248\u672c\u8fdb\u884c\u4e0b\u8f7d\uff0c\u4e5f\u5c31\u662f\u56fe\u4e2d\u7684trinityrnaseq-v2.15.1.FULL.tar.gz\u3002<\/p>\n<p>\u4e0b\u8f7d\u5b8c\u6210\u540e\u6211\u4eec\u4f7f\u7528\u5982\u4e0b\u547d\u4ee4\u8fdb\u884c\u89e3\u538b\u5b89\u88c5\uff1a<\/p>\n<p>$ tar zxvf trinityrnaseq-v2.15.1.FULL.tar.gz<\/p>\n<p>$ cd trinityrnaseq-v2.15.1<\/p>\n<p>$ make<\/p>\n<p>\u6216\u8005\u4f7f\u7528conda\u76f4\u63a5\u4e0b\u8f7d\u5b89\u88c5\uff1a<\/p>\n<p>$ conda install -c bioconda trinity<\/p>\n<ol>\n<li><strong>Trinity\u4f7f\u7528\u65b9\u6cd5<\/strong><\/li>\n<\/ol>\n<p>Trinity\u7684\u4e3b\u8981\u53c2\u6570\u5982\u4e0b\u6240\u793a\uff1a<\/p>\n<p># &#8211;seqType &lt;string&gt;: fast\u6587\u4ef6\u7c7b\u578b\uff08fa\u6216\u8005fq\uff09<\/p>\n<p># &#8211;max_memory &lt;string&gt;: \u4f7f\u7528Trinity\u8f6f\u4ef6\u65f6\u5141\u8bb8\u7684\u6700\u5927\u5185\u5b58<\/p>\n<p># \u5f53\u6570\u636e\u4e3apaired reads\u65f6\u4f7f\u7528\uff1a &#8211;left &lt;string&gt;: \u5de6\u7aefreads &#8211;right &lt;string&gt;: \u53f3\u7aefreads<\/p>\n<p># \u5f53\u6570\u636e\u4e3aunpaired reads\u65f6\u4f7f\u7528\uff1a &#8211;single &lt;string&gt;\uff1a \u6587\u4ef6\u540d<\/p>\n<p># &#8211;SS_lib_type &lt;string&gt;: \u7279\u5f02\u6027\u6587\u4ef6\u6587\u5e93\u9700\u8981\u6dfb\u52a0\u6b64\u53c2\u6570\uff0c\u5bf9\u4e8epaired reads\u6709\u4e24\u79cd\u53c2\u6570\uff08RF\u3001FR\uff09\uff1b\u5bf9\u4e8eunpaired reads\u4e5f\u6709\u4e24\u79cd\uff08F\u3001R\uff09<\/p>\n<p># &#8211;CPU &lt;int&gt;: \u6307\u5b9aCPU\u7684\u4f7f\u7528\u4e2a\u6570<\/p>\n<p>\u8ddf\u7740\u5c0f\u679c\u4e00\u8d77\u6765\u770b\u4e00\u4e2a\u4f8b\u5b50\u5427\uff01<\/p>\n<p>\u8fd0\u884c\u4e00\u4e0b\u4ee3\u7801\uff1a<\/p>\n<p>$ Trinity \u2013-seqType fq \u2013-max_memory 10G \u2013-left reads.left.fq.gz \u2013-right reads.right.fq.gz &#8211;SS_lib_type RF &#8211;CPU 4<\/p>\n<p>\u8fd0\u884c\u7ed3\u675f\u65f6\u4f1a\u81ea\u52a8\u751f\u6210\u4e00\u4e2atrinity_out_dir\u7684\u6587\u4ef6\u5939\uff0c\u91cc\u9762\u8bb0\u8f7d\u7740\u6240\u6709\u8f93\u51fa\u6587\u4ef6\uff0c\u5982\u2018trinity_out_dir.Trinity.fasta\u2019, \u5176\u4e2d\u4e00\u4e2afasta\u6761\u76ee\u5982\u4e0b\u6240\u793a\uff1a<\/p>\n<p>&gt;TRINITY_DN1000_c115_g5_i1 len=247 path=[31015:0-148 23018:149-246]<\/p>\n<p>AATCTTTTTTGGTATTGGCAGTACTGTGCTCTGGGTAGTGATTAGGGCAAAAGAAGACAC<\/p>\n<p>ACAATAAAGAACCAGGTGTTAGACGTCAGCAAGTCAAGGCCTTGGTTCTCAGCAGACAGA<\/p>\n<p>AGACAGCCCTTCTCAATCCTCATCCCTTCCCTGAACAGACATGTCTTCTGCAAGCTTCTC<\/p>\n<p>CAAGTCAGTTGTTCACAGGAACATCATCAGAATAAATTTGAAATTATGATTAGTATCTGA<\/p>\n<p>TAAAGCA<\/p>\n<p>\u2018TRINITY_DN1000_c115\u2018\u662f\u805a\u7c7b\u7684\u6807\u53f7\uff0c\u2019g5\u2018\u4ee3\u8868\u4e00\u4e2a\u57fa\u56e0\uff0c\u2019i1\u2018\u4ee3\u8868\u4e00\u4e2a\u8f6c\u5f55\u672c\u3002<\/p>\n<p>\u56e0\u4e3a\u662f\u7b97\u6cd5\u5e2e\u52a9\u6211\u4eec\u7ec4\u88c5\u7684\u8f6c\u5f55\u672c\uff0c\u6211\u4eec\u600e\u4e48\u77e5\u9053\u5b83\u7ec4\u88c5\u7684\u597d\u574f\u5462\uff1f\u63a5\u4e0b\u6765\u5c0f\u679c\u5c06\u7ee7\u7eed\u4ecb\u7ecd\u5982\u4f55\u7528\u4e0d\u540c\u65b9\u6cd5\u67e5\u770b\u8f6c\u5f55\u672c\u7684\u7ec4\u88c5\u8d28\u91cf\u3002<\/p>\n<ol>\n<li><strong>\u8ba1\u7b97\u5168\u957f\u8f6c\u5f55\u672c\u6570\u91cf<\/strong><\/li>\n<\/ol>\n<p>\u5176\u4e2d\u4e00\u79cd\u7528\u6765\u8861\u91cf\u62fc\u63a5\u8d28\u91cf\u7684\u65b9\u6cd5\u5c31\u662f\u6570\u5168\u957f\u6216\u8005\u63a5\u8fd1\u5168\u957f\u8f6c\u5f55\u672c\u7684\u6570\u91cf\uff0c\u8d8a\u591a\u4ee3\u8868\u7ec4\u88c5\u7684\u6548\u679c\u8d8a\u597d\u3002\u5bf9\u4e8e\u6a21\u5f0f\u7269\u79cd\uff0c\u6211\u4eec\u53ef\u4ee5\u5c06\u8f6c\u5f55\u672c\u6bd4\u5bf9\u5230\u53c2\u8003\u96c6\u4e0a\u53bb\uff0c\u800c\u5bf9\u4e8e\u975e\u6a21\u5f0f\u7269\u79cd\uff0c\u5982\u679c\u5b58\u5728\u6709\u9ad8\u8d28\u91cf\u6ce8\u91ca\u7684\u8fd1\u6e90\u7269\u79cd\uff0c\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528\u5b83\u4eec\u7684\u53c2\u8003\u96c6\u8fdb\u884c\u8861\u91cf\u3002<\/p>\n<p>\u6211\u4eec\u4f7f\u7528Blast+\u8fdb\u884c\u5206\u6790\uff0c\u9996\u5148\u6784\u5efa\u86cb\u767d\u8d28\u6570\u636e\u5e93<\/p>\n<p>$ makeblastdb -in uniprot_sprot.fasta -dbtype prot<\/p>\n<p>\u7136\u540e\u8fdb\u884c\u641c\u7d22<\/p>\n<p>$ blastx -query Trinity.fasta -db uniprot_sprot.fasta -out blastx.outfmt6 -evalue 1e-10 -num_threads 6 -max_target_seqs 1 -outfmt 6<\/p>\n<p>\u5f97\u5230\u4e86\u8f93\u51fa\u6587\u4ef6\u4e4b\u540e\uff0c\u6211\u4eec\u53ef\u4ee5\u4f7f\u7528Trinity\u8f6f\u4ef6\u4e4b\u4e2d\u7684\u811a\u672c\u81ea\u52a8\u5e2e\u6211\u4eec\u68c0\u6d4bTrinity\u8f6c\u5f55\u672c\u6bd4\u5bf9\u5230\u53c2\u8003\u7ec4\u4e0a\u7684\u767e\u5206\u6bd4<\/p>\n<p>$ TRINITY_HOME\/util\/analyze_blastPlus_topHit_coverage.pl blastx.outfmt6 Trinity.fasta uniprot_sprot.fasta<\/p>\n<p>\u8dd1\u5b8c\u4e4b\u540e\u6211\u4eec\u4f1a\u5f97\u5230\u4e00\u4e2a\u2019blastx.outfmt6.txt.w_pct_hit_length\u2019\u6587\u4ef6\uff0c\u901a\u8fc7\u5b83\u6211\u4eec\u53ef\u4ee5\u753b\u51fa\u4e00\u4e2a\u8868\u683c\u6765\u66f4\u597d\u7684\u5c55\u793a\u7ed3\u679c\uff0c\u5982\u4e0b\uff1a<\/p>\n<p><img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"754\" class=\"wp-image-24858\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-2.png?resize=640%2C754\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-2.png?w=730 730w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-2.png?resize=255%2C300 255w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-2.png?resize=600%2C707 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u770b\u5230\u56fe\u8868\u4e2d\u7684\u7b2c\u4e8c\u884c\uff0c\u5176\u542b\u4e49\u4e3a\u6570\u636e\u5e93\u4e2d\u6709268\u4e2a\u86cb\u767d\u8d28\u4e0eTrinity\u8f6c\u5f55\u672c\u5339\u914d\uff0c\u5339\u914d\u957f\u5ea6\u4e3a\u6bcf\u4e2a\u8f6c\u5f55\u672c\u957f\u5ea6\u768480-90%\uff1b\u6570\u636e\u5e93\u4e2d\u67093510\u4e2a\u86cb\u767d\u8d28\u53ef\u4ee5\u88ab\u51e0\u4e4e\u4e3a\u5168\u957f\u7684\u8f6c\u5f55\u672c\u8868\u793a\uff0c\u6bd4\u5bf9\u8986\u76d6\u5ea6\u5927\u4e8e80%\u3002\u7b2c\u4e00\u884c\u7684\u4fe1\u606f\u4e3a\uff0c\u67093242\u4e2a\u86cb\u767d\u8d28\u4e0e\u8f6c\u5f55\u672c\u5339\u914d\uff0c\u5339\u914d\u957f\u5ea6\u5747\u5927\u4e8e90%\u3002<\/p>\n<ol>\n<li><strong>RNA Seq Read Representation<\/strong><\/li>\n<\/ol>\n<p>\u53e6\u5916\u4e00\u79cd\u65b9\u6cd5\u662f\u4e3a\u4e86\u68c0\u6d4bRNA seq reads\u80fd\u5426\u8f83\u597d\u7684\u8868\u793aTrinity\u7ec4\u88c5\u7684\u8f6c\u5f55\u672c\uff0c\u4e3a\u4e86\u5168\u9762\u6355\u83b7reads\uff0c\u6211\u4eec\u4f7f\u7528Bowtie2\u5c06reads\u548c\u8f6c\u5f55\u7ec4\u5bf9\u9f50\uff0c\u7136\u540e\u8ba1\u7b97\u6b63\u786e\u7684\u4e0d\u6b63\u786e\u7684\u548c\u88ab\u5b64\u7acb\u7684reads\u7684\u6570\u91cf<\/p>\n<p>\u9996\u5148\uff0c\u6211\u4eec\u4e3a\u8f6c\u5f55\u672c\u5efa\u7acb\u7d22\u5f15<\/p>\n<p>$ bowtie2-build Trinity.fasta Trinity.fasta<\/p>\n<p>\u7136\u540e\u8fdb\u884c\u6bd4\u5bf9\u6765\u83b7\u53d6read\u7684\u6bd4\u5bf9\u4fe1\u606f, \u6211\u4eec\u4ee5\u53cc\u7aef\u6570\u636e\u4e3a\u4f8b<\/p>\n<p>$ bowtie2 -p 10 -q &#8211;no-unal -k 20 -x Trinity.fasta -1 reads_1.fq -2 reads_2.fq 2&gt;align_stats.txt| samtools view -@10 -Sb -o bowtie2.bam<\/p>\n<p>\u6700\u540e\u53ef\u4ee5\u67e5\u770b\u8f93\u51fa\u6587\u4ef6\u2019align_stats.txt\u2019<\/p>\n<p>$ cat 2&gt;&amp;1 align_stats.txt<\/p>\n<p>\u7ed3\u679c\u5982\u4e0b\u6240\u793a\uff1a <img decoding=\"async\" loading=\"lazy\" width=\"640\" height=\"329\" class=\"wp-image-24859\" src=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-3.png?resize=640%2C329\" srcset=\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-3.png?w=1127 1127w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-3.png?resize=300%2C154 300w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-3.png?resize=1024%2C527 1024w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-3.png?resize=768%2C395 768w, https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/word-image-24856-3.png?resize=600%2C309 600w\" sizes=\"(max-width: 640px) 100vw, 640px\" data-recalc-dims=\"1\" \/><\/p>\n<p>\u6211\u4eec\u53ef\u4ee5\u770b\u5230\u670989.97%\u7684\u6bd4\u5bf9\u7387\uff0c\u603b\u7684\u6765\u8bf4\u5bf9\u4e8e\u53cc\u7aef\u6570\u636e\uff0c\u670970~80%\u7684\u6bd4\u5bf9\u7387\u5c31\u7b97\u5408\u683c\u4e86\u3002<\/p>\n<p>\u597d\u4e86\u4eca\u5929\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u5566~\u6709\u4ec0\u4e48\u95ee\u9898\u53ef\u4ee5\u548c\u5c0f\u679c\u4e00\u8d77\u8ba8\u8bba\u54e6~\u4e0b\u4e00\u671f\u5c0f\u679c\u7ee7\u7eed\u4e3a\u5927\u5bb6\u5e26\u6765Trinity\u7684\u66f4\u591a\u540e\u7eed\u5185\u5bb9\u54e6<\/p>\n<p>\u66f4\u591a\u751f\u4fe1\u5c0f\u5de5\u5177\u53ef\u67e5\u8be2\u4e91\u5e73\u53f0\uff1ahttp:\/\/www.biocloudservice.com\/home.html<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Trinity, \u662f\u7531Broad Institute\u5f00\u53d1\u7684\u8fdb\u884cde novo\u8f6c\u5f55\u672c\u7ec4\u88c5\u7684\u5de5\u5177\uff0c\u5b83\u80fd\u5c06RNA-s 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