{"id":2042,"date":"2022-06-08T11:55:36","date_gmt":"2022-06-08T15:55:36","guid":{"rendered":"http:\/\/sys4seq.com\/?page_id=2042"},"modified":"2022-06-08T11:55:36","modified_gmt":"2022-06-08T15:55:36","slug":"transcriptomics","status":"publish","type":"page","link":"https:\/\/sys4seq.com\/index.php\/transcriptomics\/","title":{"rendered":"Transcriptomics"},"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\/2022\/06\/08\/spatial-gene-expression-data-analysis-on-cluster-10x-genomics-space-ranger\/\" title=\"Spatial gene expression data analysis on Cluster  : 10X Genomics, Space Ranger\">Spatial gene expression data analysis on Cluster  : 10X Genomics, Space Ranger<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2022-06-08T12:00:38-04:00\">June 8, 2022<\/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\/omics\/\">Omics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/transcriptomics\/\">Transcriptomics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">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,<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2022\/06\/08\/spatial-gene-expression-data-analysis-on-cluster-10x-genomics-space-ranger\/\" 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\/10x-genomics\/\">10X Genomics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/space-ranger\/\">Space Ranger<\/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\/2021\/05\/03\/single-cell-gene-expression-data-analysis-on-cluster-10x-genomics-cell-ranger\/\" title=\"Single cell gene expression data analysis on Cluster : 10X Genomics, Cell Ranger\">Single cell gene expression data analysis on Cluster : 10X Genomics, Cell Ranger<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2021-05-03T12:17:33-04:00\">May 3, 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\/omics\/\">Omics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/transcriptomics\/\">Transcriptomics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">Cell Ranger can be run in cluster mode, using job schedulers like Sun Grid Engine (or simply SGE) or Load Sharing Facility (or simply LSF) as queuing system allows highly parallelizable jobs. &gt;&gt;&gt;<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2021\/05\/03\/single-cell-gene-expression-data-analysis-on-cluster-10x-genomics-cell-ranger\/\" 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\/10x-genomics\/\">10X Genomics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/cellranger\/\">Cellranger<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/scrna-seq\/\">scRNA-seq<\/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\/2019\/10\/29\/a-multi-tiered-rna-seq-analyses-approach-to-clinical-diagnosis-of-a-genetic-disease\/\" title=\"A multi-tiered RNA-seq analyses approach to clinical diagnosis of a genetic disease\">A multi-tiered RNA-seq analyses approach to clinical diagnosis of a genetic disease<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2019-10-29T12:21:43-04:00\">October 29, 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\/omics\/\">Omics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/transcriptomics\/\">Transcriptomics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">A novel three-tiered approach of targeted RNA-seq analysis for molecular diagnosis of a genetic disease (ex. neuromuscular disease; NMD) was proposed. Analysis will be stopped if molecular diagnosis is achieved in any of the Tiers and the results will be clinically correlated to reclassify variants of uncertain significance (VUSs), identify pathogenic events at the mRNA<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2019\/10\/29\/a-multi-tiered-rna-seq-analyses-approach-to-clinical-diagnosis-of-a-genetic-disease\/\" 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\/rna-seq\/\">RNA-seq<\/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\/2018\/03\/20\/rna-seq-raw-reads-to-differential-expression\/\" title=\"RNA-Seq : raw reads to differential expression\">RNA-Seq : raw reads to differential expression<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2018-03-20T12:04:32-04:00\">March 20, 2018<\/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\/omics\/\">Omics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/transcriptomics\/\">Transcriptomics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">A simple RNA-Seq differential expression analysis using High Performance Computing (HPC). &gt;&gt;&gt;<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2018\/03\/20\/rna-seq-raw-reads-to-differential-expression\/\" 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\/rna-seq\/\">RNA-seq<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/star\/\">STAR<\/a><\/span><\/footer><\/div><\/div><!--\/.cherry-posts-item--><div class=\"cherry-posts-item post-item item-4 odd\"><div class=\"inner cherry-clearfix\"><figure class=\"post-thumbnail\"><\/figure>\n<h4 class=\"post-title\"><a href=\"https:\/\/sys4seq.com\/index.php\/2018\/01\/05\/genomic-variants-from-rna-seq-data\/\" title=\"Genomic variants from RNA-seq data\">Genomic variants from RNA-seq data<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2018-01-05T12:08:06-04:00\">January 5, 2018<\/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\/omics\/\">Omics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/transcriptomics\/\">Transcriptomics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">RNA-Seq allows the detection and quantification of known and rare RNA transcripts within a sample. In addition to differential expression and detection of novel transcripts, RNA-seq also supports the detection of genomic variation in expressed regions. &gt;&gt;&gt;<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2018\/01\/05\/genomic-variants-from-rna-seq-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\/rna-seq\/\">RNA-seq<\/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-5 even\"><div class=\"inner cherry-clearfix\"><figure class=\"post-thumbnail\"><\/figure>\n<h4 class=\"post-title\"><a href=\"https:\/\/sys4seq.com\/index.php\/2017\/12\/17\/eqtl-analysis-of-rna-seq-data\/\" title=\"eQTL analysis of RNA-seq data\">eQTL analysis of RNA-seq data<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2017-12-17T12:10:16-04:00\">December 17, 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\/omics\/\">Omics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/transcriptomics\/\">Transcriptomics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">Genetic locus that affects gene expression is often referred to as expression quantitative trait locus (eQTL). eQTL mapping studies assesses the association of SNPs with genome-wide expression levels. &gt;&gt;&gt;<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2017\/12\/17\/eqtl-analysis-of-rna-seq-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\/rna-seq\/\">RNA-seq<\/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\/2042"}],"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=2042"}],"version-history":[{"count":1,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/pages\/2042\/revisions"}],"predecessor-version":[{"id":2044,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/pages\/2042\/revisions\/2044"}],"wp:attachment":[{"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/media?parent=2042"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}