{"id":2047,"date":"2022-06-08T12:00:38","date_gmt":"2022-06-08T16:00:38","guid":{"rendered":"http:\/\/sys4seq.com\/?p=2047"},"modified":"2022-06-08T12:01:20","modified_gmt":"2022-06-08T16:01:20","slug":"spatial-gene-expression-data-analysis-on-cluster-10x-genomics-space-ranger","status":"publish","type":"post","link":"https:\/\/sys4seq.com\/index.php\/2022\/06\/08\/spatial-gene-expression-data-analysis-on-cluster-10x-genomics-space-ranger\/","title":{"rendered":"Spatial gene expression data analysis on Cluster  : 10X Genomics, Space Ranger"},"content":{"rendered":"<p>Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing.<\/p>\n<p>There are 2 steps to analyze Spatial RNA-seq data<sup id=\"fnref:1\" role=\"doc-noteref\"><\/sup>.<\/p>\n<p><strong>Step 1<\/strong>: <code class=\"language-plaintext highlighter-rouge\">spaceranger mkfastq<\/code> demultiplexes raw base call (<code class=\"language-plaintext highlighter-rouge\">BCL<\/code>) files generated by Illumina sequencers into FASTQ files.<br \/>\n<strong>Step 2<\/strong>: <code class=\"language-plaintext highlighter-rouge\">spaceranger count<\/code> takes FASTQ files from <code class=\"language-plaintext highlighter-rouge\">spaceranger mkfastq<\/code> and performs alignment, filtering, barcode counting, and UMI counting.<\/p>\n<p><a href=\"https:\/\/adinasarapu.github.io\/posts\/2020\/03\/blog-spatial-gene-expression\/\">&gt;&gt;&gt;<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"Running spaceranger as cluster mode that uses Sun Grid Engine (SGE) as queuing. There are 2 steps to analyze Spatial RNA-seq data. Step 1: spaceranger mkfastq demultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files. Step 2: spaceranger count takes FASTQ files from spaceranger mkfastq and performs alignment, filtering, barcode counting,","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_mi_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0},"categories":[11,63,70],"tags":[71,72],"_links":{"self":[{"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/posts\/2047"}],"collection":[{"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/types\/post"}],"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=2047"}],"version-history":[{"count":2,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/posts\/2047\/revisions"}],"predecessor-version":[{"id":2049,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/posts\/2047\/revisions\/2049"}],"wp:attachment":[{"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/media?parent=2047"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/categories?post=2047"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/tags?post=2047"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}