{"id":2039,"date":"2022-06-08T11:55:17","date_gmt":"2022-06-08T15:55:17","guid":{"rendered":"http:\/\/sys4seq.com\/?page_id=2039"},"modified":"2022-06-08T11:55:17","modified_gmt":"2022-06-08T15:55:17","slug":"genomics","status":"publish","type":"page","link":"https:\/\/sys4seq.com\/index.php\/genomics\/","title":{"rendered":"Genomics"},"content":{"rendered":"<div id=\"cherry-posts-list-1\" class=\"cherry-posts-list template-default  \"><div class=\"cherry-posts-item post-item item-0 odd\"><div class=\"inner cherry-clearfix\"><figure class=\"post-thumbnail\"><\/figure>\n<h4 class=\"post-title\"><a href=\"https:\/\/sys4seq.com\/index.php\/2021\/04\/13\/annotation-of-genetic-variants\/\" title=\"Annotation of genetic variants\">Annotation of genetic variants<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2021-04-13T11:58:34-04:00\">April 13, 2021<\/time> by <span class=\"post-author vcard\"><a href=\"https:\/\/sys4seq.com\/index.php\/author\/adinasarapu\/\" rel=\"author\">Ashok Dinasarapu<\/a><\/span>  <span class=\"post-tax post-tax-category\"><a href=\"https:\/\/sys4seq.com\/index.php\/category\/analysis\/\">Analysis<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/genomics\/\">Genomics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/omics\/\">Omics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file. &gt;&gt;&gt;<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2021\/04\/13\/annotation-of-genetic-variants\/\" class=\"btn btn-default\">read more<\/a>\n<footer><span class=\"post-tax post-tax-post_tag\"><a href=\"https:\/\/sys4seq.com\/index.php\/tag\/annotation\/\">Annotation<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/variants\/\">Variants<\/a><\/span><\/footer><\/div><\/div><!--\/.cherry-posts-item--><div class=\"cherry-posts-item post-item item-1 even\"><div class=\"inner cherry-clearfix\"><figure class=\"post-thumbnail\"><\/figure>\n<h4 class=\"post-title\"><a href=\"https:\/\/sys4seq.com\/index.php\/2019\/12\/05\/atac-seq-peak-calling-with-macs2\/\" title=\"ATAC-seq peak calling with MACS2\">ATAC-seq peak calling with MACS2<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2019-12-05T12:02:09-04:00\">December 5, 2019<\/time> by <span class=\"post-author vcard\"><a href=\"https:\/\/sys4seq.com\/index.php\/author\/adinasarapu\/\" rel=\"author\">Ashok Dinasarapu<\/a><\/span>  <span class=\"post-tax post-tax-category\"><a href=\"https:\/\/sys4seq.com\/index.php\/category\/analysis\/\">Analysis<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/genomics\/\">Genomics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/omics\/\">Omics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility. &gt;&gt;&gt;<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2019\/12\/05\/atac-seq-peak-calling-with-macs2\/\" class=\"btn btn-default\">read more<\/a>\n<footer><span class=\"post-tax post-tax-post_tag\"><a href=\"https:\/\/sys4seq.com\/index.php\/tag\/atac-seq\/\">ATAC-seq<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/macs2\/\">MACS2<\/a><\/span><\/footer><\/div><\/div><!--\/.cherry-posts-item--><div class=\"cherry-posts-item post-item item-2 odd\"><div class=\"inner cherry-clearfix\"><figure class=\"post-thumbnail\"><\/figure>\n<h4 class=\"post-title\"><a href=\"https:\/\/sys4seq.com\/index.php\/2017\/12\/16\/quality-control-for-gwas-studies\/\" title=\"Quality control for GWAS studies\">Quality control for GWAS studies<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2017-12-16T12:12:18-04:00\">December 16, 2017<\/time> by <span class=\"post-author vcard\"><a href=\"https:\/\/sys4seq.com\/index.php\/author\/adinasarapu\/\" rel=\"author\">Ashok Dinasarapu<\/a><\/span>  <span class=\"post-tax post-tax-category\"><a href=\"https:\/\/sys4seq.com\/index.php\/category\/analysis\/\">Analysis<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/genomics\/\">Genomics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/omics\/\">Omics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">An important step in the analysis of genome-wide association studies (GWAS) is to identify problematic subjects and markers. Quality control (QC) in GWAS removes markers and individuals, and greatly increases the accuracy of findings. &gt;&gt;&gt;<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2017\/12\/16\/quality-control-for-gwas-studies\/\" class=\"btn btn-default\">read more<\/a>\n<footer><span class=\"post-tax post-tax-post_tag\"><a href=\"https:\/\/sys4seq.com\/index.php\/tag\/qc\/\">QC<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/variants\/\">Variants<\/a><\/span><\/footer><\/div><\/div><!--\/.cherry-posts-item--><div class=\"cherry-posts-item post-item item-3 even\"><div class=\"inner cherry-clearfix\"><figure class=\"post-thumbnail\"><\/figure>\n<h4 class=\"post-title\"><a href=\"https:\/\/sys4seq.com\/index.php\/2017\/08\/19\/copy-number-variation-discovery-workflows-using-ngs-data\/\" title=\"Copy number variation discovery workflows using NGS data\">Copy number variation discovery workflows using NGS data<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2017-08-19T12:14:30-04:00\">August 19, 2017<\/time> by <span class=\"post-author vcard\"><a href=\"https:\/\/sys4seq.com\/index.php\/author\/adinasarapu\/\" rel=\"author\">Ashok Dinasarapu<\/a><\/span>  <span class=\"post-tax post-tax-category\"><a href=\"https:\/\/sys4seq.com\/index.php\/category\/analysis\/\">Analysis<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/genomics\/\">Genomics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/omics\/\">Omics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">Copy number variations (CNVs) represent gain or loss of genomic regions. CNVs transmit from parents to offspring or arise de novo and play important role in neuro-psychiatric disorders and cancers. &gt;&gt;&gt;<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2017\/08\/19\/copy-number-variation-discovery-workflows-using-ngs-data\/\" class=\"btn btn-default\">read more<\/a>\n<footer><span class=\"post-tax post-tax-post_tag\"><a href=\"https:\/\/sys4seq.com\/index.php\/tag\/cnv\/\">CNV<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/variants\/\">Variants<\/a><\/span><\/footer><\/div><\/div><!--\/.cherry-posts-item--><\/div><!--\/.cherry-posts-list-->\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_mi_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0},"_links":{"self":[{"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/pages\/2039"}],"collection":[{"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/comments?post=2039"}],"version-history":[{"count":1,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/pages\/2039\/revisions"}],"predecessor-version":[{"id":2041,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/pages\/2039\/revisions\/2041"}],"wp:attachment":[{"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/media?parent=2039"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}