{"id":2004,"date":"2022-06-08T11:09:37","date_gmt":"2022-06-08T15:09:37","guid":{"rendered":"http:\/\/sys4seq.com\/?page_id=2004"},"modified":"2022-06-08T11:50:25","modified_gmt":"2022-06-08T15:50:25","slug":"blog_omics","status":"publish","type":"page","link":"https:\/\/sys4seq.com\/index.php\/blog_omics\/","title":{"rendered":"Omics"},"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\/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 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\/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-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\/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 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\/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-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\/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-5 even\"><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-6 odd\"><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-7 even\"><div class=\"inner cherry-clearfix\"><figure class=\"post-thumbnail\"><\/figure>\n<h4 class=\"post-title\"><a href=\"https:\/\/sys4seq.com\/index.php\/2020\/04\/04\/quantitative-proteomics-label-free-quantitation-of-proteins\/\" title=\"Quantitative proteomics: label-free quantitation of proteins\">Quantitative proteomics: label-free quantitation of proteins<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2020-04-04T11:12:19-04:00\">April 4, 2020<\/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\/proteomics\/\">Proteomics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">Liquid chromatography (LC) coupled with mass spectrometry (MS) has been widely used for protein expression quantification. Protein quantification by tandem-MS (MS\/MS) uses integrated peak intensity from the parent-ion mass (MS1) or features from fragment-ions (MS2).\u00a0Label-free quantification (LFQ) may be based on precursor ion intensity (peak areas or peak heights) or on spectral counting. Here, the<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2020\/04\/04\/quantitative-proteomics-label-free-quantitation-of-proteins\/\" 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\/lfq\/\">LFQ<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/omics\/\">Omics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/proteomics\/\">Proteomics<\/a><\/span><\/footer><\/div><\/div><!--\/.cherry-posts-item--><div class=\"cherry-posts-item post-item item-8 odd\"><div class=\"inner cherry-clearfix\"><figure class=\"post-thumbnail\"><\/figure>\n<h4 class=\"post-title\"><a href=\"https:\/\/sys4seq.com\/index.php\/2020\/04\/04\/quantitative-proteomics-tmt-based-quantitation-of-proteins\/\" title=\"Quantitative proteomics : TMT-based quantitation of proteins\">Quantitative proteomics : TMT-based quantitation of proteins<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2020-04-04T11:21:06-04:00\">April 4, 2020<\/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\/proteomics\/\">Proteomics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">Quantification of proteins using isobaric labeling (tandem mass tag or TMT) starts with the reduction of disulfide bonds in proteins with Dithiothreitol (DTT).\u00a0Alkylation with iodoacetamide (IAA) after cystine reduction results in the covalent addition of a carbamidomethyl group that prevents the formation of disulfide bonds. Then, overnight digestion of the proteins using trypsin or trypsin\/LyC<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2020\/04\/04\/quantitative-proteomics-tmt-based-quantitation-of-proteins\/\" 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\/omics\/\">Omics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/proteomics\/\">Proteomics<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/tag\/tmt\/\">TMT<\/a><\/span><\/footer><\/div><\/div><!--\/.cherry-posts-item--><div class=\"cherry-posts-item post-item item-9 even\"><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-10 odd\"><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-11 even\"><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\/taxonomic-and-diversity-profiling-of-the-microbiome-16s-rrna-gene-amplicon-sequence-data\/\" title=\"Taxonomic and diversity profiling of the microbiome : 16S rRNA gene amplicon sequence data\">Taxonomic and diversity profiling of the microbiome : 16S rRNA gene amplicon sequence data<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2022-06-08T11:46:32-04:00\">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\/microbiome\/\">Microbiome<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/omics\/\">Omics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">The 16S ribosomal RNA (rRNA) gene of Bacteria codes for the RNA component of the 30S subunit. Different bacterial species have one to multiple copies of the 16S rRNA gene, and each with 9 hypervariable regions, V1-V9. High-throughput sequencing of 16S rRNA gene (a \u201cmarker gene\u201d) amplicons has become a widely used method to study<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2022\/06\/08\/taxonomic-and-diversity-profiling-of-the-microbiome-16s-rrna-gene-amplicon-sequence-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\/microbiome\/\">Microbiome<\/a><\/span><\/footer><\/div><\/div><!--\/.cherry-posts-item--><div class=\"cherry-posts-item post-item item-12 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\/taxonomic-and-functional-profiling-of-the-microbiome-whole-genome-shotgun-metagenomics\/\" title=\"Taxonomic and functional profiling of the microbiome &#8211; whole genome shotgun metagenomics\">Taxonomic and functional profiling of the microbiome &#8211; whole genome shotgun metagenomics<\/a><\/h4>\n<div class=\"post-meta\">\n\tPosted on <time datetime=\"2022-06-08T11:48:15-04:00\">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\/microbiome\/\">Microbiome<\/a> <a href=\"https:\/\/sys4seq.com\/index.php\/category\/omics\/\">Omics<\/a><\/span>\n<\/div>\n\n<div class=\"post-content part\">This workflow consists of taxonomic and functional profiling of shotgun metagenomics sequencing (MGS) reads using MetaPhlAn2 and HUMAnN2, respectively. To perform taxonomic (phyla, genera or species level) profiling of the MGS data, the MetaPhlAn2 pipeline was run on a high performance multicore cluster computing environment. &gt;&gt;&gt;<\/div>\n<a href=\"https:\/\/sys4seq.com\/index.php\/2022\/06\/08\/taxonomic-and-functional-profiling-of-the-microbiome-whole-genome-shotgun-metagenomics\/\" 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\/microbiome\/\">Microbiome<\/a><\/span><\/footer><\/div><\/div><!--\/.cherry-posts-item--><div class=\"cherry-posts-item post-item item-13 even\"><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><!--\/.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\/2004"}],"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=2004"}],"version-history":[{"count":6,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/pages\/2004\/revisions"}],"predecessor-version":[{"id":2037,"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/pages\/2004\/revisions\/2037"}],"wp:attachment":[{"href":"https:\/\/sys4seq.com\/index.php\/wp-json\/wp\/v2\/media?parent=2004"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}