{"id":187,"date":"2024-07-23T18:30:07","date_gmt":"2024-07-23T10:30:07","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=187"},"modified":"2025-12-12T15:58:35","modified_gmt":"2025-12-12T07:58:35","slug":"hla-hd","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2024\/07\/23\/hla-hd\/","title":{"rendered":"HLA-HD"},"content":{"rendered":"<h2>1. \u8f6f\u4ef6\u5b89\u88c5<\/h2>\n<h3>1.1 conda \u5b89\u88c5bowtie2<\/h3>\n<p>conda create -n bowtie2<br \/>\nconda activate bowtie2<br \/>\nconda install bioconda::bowtie2<\/p>\n<h3>1.2 \u5b98\u7f51\u4e0b\u8f7dHLA-HD\u8f6f\u4ef6\u5e76\u89e3\u538b<\/h3>\n<p><a href=\"https:\/\/www.genome.med.kyoto-u.ac.jp\/HLA-HD\/\">https:\/\/www.genome.med.kyoto-u.ac.jp\/HLA-HD\/<\/a><br \/>\n\u89e3\u538b\u540e\u8fd0\u884c sh install.sh<br \/>\nbin\u6587\u4ef6\u5939\u4e0b\u7684\u6240\u6709sh\u811a\u672c\u8fdb\u884cchmod 777\uff0c\u4e4b\u540e\u5c06bin\u6587\u4ef6\u5939\u8def\u5f84\u6dfb\u52a0\u5165~\/.bashrc<\/p>\n<h3>1.3 \u66f4\u65b0HLA\u5e93<\/h3>\n<p>sh update.dictionary.sh<\/p>\n<h3>1.4 \u8fd0\u884c\u524d\u51c6\u5907<\/h3>\n<pre><code>ulimit -Sa \n# \u67e5\u770bopen files\u53c2\u6570\uff0c\u5982\u679c&lt;1024\u5219\uff1a\nulimit -n 1024<\/code><\/pre>\n<h2>2. \u6784\u5efa\u6279\u91cf\u8fd0\u884c\u811a\u672c<\/h2>\n<pre><code class=\"language-bash\">mkdir HLA_HD\ncd HLA_HD\nconda activate HLA_HD\n\n# \u8001perl\u7248\nls ..\/rawdata\/*.R1.clean.fastq.gz|perl -ne &#039;chomp;my $name=$1 if($_=~\/\\\/([^\\\/]+)\\.R1\/);print &quot;hlahd -t 2 -m 100 -c 0.95 -f \/data02\/zhangmengmeng\/software\/hlahd.1.7.0\/freq_data ..\/rawdata\/$name\\.R1.clean.fastq.gz ..\/rawdata\/$name\\.R2.clean.fastq.gz \/data02\/zhangmengmeng\/software\/hlahd.1.7.0\/HLA_gene.split.txt \/data02\/zhangmengmeng\/software\/hlahd.1.7.0\/dictionary $name .\/ &amp;&amp; echo $name ok\\n&quot;&#039; &gt;hlahd.sh\n\n# \u65b0shell\u547d\u4ee4\nfor r1 in ..\/rawdata\/*_R1.fastq.gz; do name=$(basename &quot;$r1&quot; _R1.fastq.gz); echo &quot;hlahd.sh -t 2 -m 100 -c 0.95 -f \/home\/zhoukaiwen\/software\/hlahd.1.7.1\/freq_data ..\/rawdata\/${name}_R1.fastq.gz ..\/rawdata\/${name}_R2.fastq.gz \/home\/zhoukaiwen\/software\/hlahd.1.7.1\/HLA_gene.split.txt \/home\/zhoukaiwen\/software\/hlahd.1.7.1\/dictionary $name .\/ &amp;&amp; echo $name ok&quot;; done &gt; hlahd.sh\n<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. \u8f6f\u4ef6\u5b89\u88c5 1.1 conda \u5b89\u88c5bowtie2 conda create -n bowtie2 con&#8230;<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"class_list":["post-187","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"_links":{"self":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/187","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/comments?post=187"}],"version-history":[{"count":7,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/187\/revisions"}],"predecessor-version":[{"id":665,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/187\/revisions\/665"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=187"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=187"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=187"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}