{"id":143,"date":"2023-07-11T13:03:47","date_gmt":"2023-07-11T05:03:47","guid":{"rendered":"https:\/\/www.kz-hub.tech\/?p=143"},"modified":"2023-07-11T13:12:18","modified_gmt":"2023-07-11T05:12:18","slug":"ascat-cnv","status":"publish","type":"post","link":"https:\/\/www.kz-hub.tech\/index.php\/2023\/07\/11\/ascat-cnv\/","title":{"rendered":"ASCAT &#8211; CNV\u6279\u91cf\u811a\u672c"},"content":{"rendered":"<h5>\u6784\u5efaascat_example.R\uff0c\u7528\u4e8e\u540e\u7eed\u6bcf\u4e2a\u6837\u672c\u7684\u6a21\u677f<\/h5>\n<pre><code class=\"language-R\">library(ASCAT)\n\nascat.prepareHTS(\n  tumourseqfile = &quot;\/home\/zhoukaiwen\/IBC\/WES\/align\/Tumor_name_bqsr.bam&quot;,\n  normalseqfile = &quot;\/home\/zhoukaiwen\/IBC\/WES\/align\/Normal_name_bqsr.bam&quot;,\n  tumourname = &quot;Tumor_name&quot;,\n  normalname = &quot;Normal_name&quot;,\n  allelecounter_exe = &quot;\/home\/zhoukaiwen\/software\/anaconda3\/bin\/alleleCounter&quot;,\n  alleles.prefix = &quot;\/home\/zhoukaiwen\/database\/G1000_allelesAll_hg19\/G1000_alleles_hg19_chr&quot;,\n  loci.prefix = &quot;\/home\/zhoukaiwen\/database\/G1000_lociAll_hg19\/G1000_loci_hg19_chr&quot;,\n  gender = &quot;XX&quot;,\n  genomeVersion = &quot;hg19&quot;,\n  nthreads = 4,\n  tumourLogR_file = &quot;Tumor_name_LogR.txt&quot;,\n  tumourBAF_file = &quot;Tumor_name_BAF.txt&quot;,\n  normalLogR_file = &quot;Normal_name_LogR.txt&quot;,\n  normalBAF_file = &quot;Normal_name_BAF.txt&quot;)\n\nascat.bc = ascat.loadData(Tumor_LogR_file = &quot;Tumor_name_LogR.txt&quot;, Tumor_BAF_file = &quot;Tumor_name_BAF.txt&quot; Germline_LogR_file = &quot;Normal_name_LogR.txt&quot;, Germline_BAF_file = &quot;Normal_name_BAF.txt&quot;, gender = &#039;XX&#039;, genomeVersion = &quot;hg19&quot;)\nascat.plotRawData(ascat.bc, img.prefix = &quot;Before_correction_&quot;)\nascat.bc = ascat.correctLogR(ascat.bc, GCcontentfile = &quot;\/home\/zhoukaiwen\/database\/GC_G1000_hg19.txt&quot;, replictimingfile = &quot;\/home\/zhoukaiwen\/database\/RT_G1000_hg19.txt&quot;)\nascat.plotRawData(ascat.bc, img.prefix = &quot;After_correction_&quot;)\nascat.bc = ascat.aspcf(ascat.bc)\nascat.plotSegmentedData(ascat.bc)\nascat.output = ascat.runAscat(ascat.bc, gamma=1, write_segments = T)\nQC = ascat.metrics(ascat.bc,ascat.output)\nsave(ascat.bc, ascat.output, QC, file = &#039;Tumor_name_ASCAT_objects.Rdata&#039;)<\/code><\/pre>\n<h5>\u6784\u5efashell\u811a\u672c\u7528\u4e8e\u6279\u91cf\u8fd0\u884cASCAT<\/h5>\n<pre><code class=\"language-bash\">for n in `ls ..\/align\/*-T_bqsr.bam|sed &#039;s\/\\.\\.\\\/align\\\/\/\/g&#039;|sed &#039;s\/\\_bqsr\\.bam\/\/g&#039;|sed &#039;s\/\\-T\/\/g&#039;`; do echo cp ascat_example.R $n\\_RunAscat.R \\&amp;\\&amp; sed -i \\&#039;s\/Tumor\\_name\/$n-T\/g\\&#039; $n\\_RunAscat.R \\&amp;\\&amp; sed -i \\&#039;s\/Normal\\_name\/$n-B\/g\\&#039; $n\\_RunAscat.R \\&amp;\\&amp; Rscript $n\\_RunAscat.R \\&amp;\\&amp; echo $n ASCAT Done &gt;&gt; CreateASCATRscript.sh;done<\/code><\/pre>\n<h5>\u5c06ASCAT\u7ed3\u679c\u7684segment.txt \u8f6c\u6362\u4e3aGISTIC input<\/h5>\n<pre><code class=\"language-R\"><\/code><\/pre>\n","protected":false},"excerpt":{"rendered":"<p>\u6784\u5efaascat_example.R\uff0c\u7528\u4e8e\u540e\u7eed\u6bcf\u4e2a\u6837\u672c\u7684\u6a21\u677f library(ASCAT) ascat.prep&#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-143","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\/143","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=143"}],"version-history":[{"count":3,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/143\/revisions"}],"predecessor-version":[{"id":146,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/posts\/143\/revisions\/146"}],"wp:attachment":[{"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/media?parent=143"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/categories?post=143"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kz-hub.tech\/index.php\/wp-json\/wp\/v2\/tags?post=143"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}