{"id":506,"date":"2025-03-10T17:48:24","date_gmt":"2025-03-10T09:48:24","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=506"},"modified":"2025-03-10T20:01:49","modified_gmt":"2025-03-10T12:01:49","slug":"scarhrd","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2025\/03\/10\/scarhrd\/","title":{"rendered":"scarHRD"},"content":{"rendered":"<h3>1. \u8fdb\u5165\u865a\u62df\u73af\u5883\u5e76\u5b89\u88c5sequenza<\/h3>\n<p>scarHRD\u9700\u8981sequenza\u7684\u7ed3\u679c\u6587\u4ef6\u8fd0\u884c<\/p>\n<pre><code class=\"language-bash\">conda activate sequenza\n\nR\nlibrary(devtools)\ninstall_github(&#039;sztup\/scarHRD&#039;,build_vignettes = TRUE)\ninstall_github(&#039;aroneklund\/copynumber&#039;)<\/code><\/pre>\n<h3>2. \u6784\u5efa\u6309\u6837\u672c\u8fd0\u884cscarHRD\u7684R\u811a\u672c<\/h3>\n<p><strong><em>EXAMPLE_scarHRD.R<\/em><\/strong><\/p>\n<pre><code class=\"language-R\">library(copynumber)\nlibrary(sequenza)\nlibrary(scarHRD)\nscar_score(&quot;\/data02\/zhangmengmeng\/BPT\/LCM-WES\/sequenza\/EXAMPLE.small.seqz.gz&quot;,reference = &quot;grch38&quot;, seqz=TRUE)<\/code><\/pre>\n<p><strong>\u8fd0\u884cscarHRD :<\/strong><br \/>\n<strong><em>RunScarHRD.sh<\/em><\/strong><\/p>\n<pre><code>#!\/bin\/bash\n\n# Directory containing the .seqz.gz files\ninput_dir=&quot;..\/sequenza&quot;\n\n# Loop through each .seqz.gz file in the directory\nfor file in $input_dir\/*small.seqz.gz; do\n    # Extract the base name without path and extension\n    sample_name=$(basename &quot;$file&quot; .small.seqz.gz)\n\n    # Create the necessary commands and run them\n    cp .\/EXAMPLE_scarHRD.R $sample_name.R\n    sed -i &quot;s\/EXAMPLE\/$sample_name\/&quot; $sample_name.R\n    Rscript $sample_name.R\n    echo &quot;$sample_name scarHRD ok&quot;\ndone<\/code><\/pre>\n<p><strong><em>\u5408\u5e76\u7ed3\u679c\u6587\u4ef6<\/em><\/strong><\/p>\n<pre><code>awk &#039;FNR==1 &amp;&amp; NR!=1 {next} {print}&#039; *.small.seqz._HRDresults.txt &gt; All_HRDresults.txt<\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>1. \u8fdb\u5165\u865a\u62df\u73af\u5883\u5e76\u5b89\u88c5sequenza scarHRD\u9700\u8981sequenza\u7684\u7ed3\u679c\u6587\u4ef6\u8fd0\u884c conda act&#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-506","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\/506","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=506"}],"version-history":[{"count":5,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/506\/revisions"}],"predecessor-version":[{"id":511,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/506\/revisions\/511"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=506"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=506"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=506"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}