PPT-RNAseq

Author : olivia-moreira | Published Date : 2017-11-03

transcriptome RNA seq reads Illumina sequencing mRNA RNA Seq Alignment 35bp 150bp s ingle or pairedend reads RNA seq alignments Wang K et al MapSplice Accurate

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RNAseq: Transcript

transcriptome RNA seq reads Illumina sequencing mRNA RNA Seq Alignment 35bp 150bp s ingle or pairedend reads RNA seq alignments Wang K et al MapSplice Accurate Mapping of RNA. Ramesh . Hariharan. Strand Life Sciences. IISc. What is Read Alignment?. AGGCTACGCATTTCCCATAAAGACCCACGCTTAAGTTC. Subject’s Genome. AGGCTACGCAT. G. TCCCATAA. T. GACCCAC. A. CTTAAGTTC. Reference Genome. . RNASeq. Pipeline. Steve Searle. Outline of Talk. What the . Ensembl. . RNASeq. pipeline does. Ensembl. Pipeline infrastructure. How we’ve modified the process as its scaled . up. Cloud version. Genome Browser. Combines a genome database with interactive web pages. Allows the user to retrieve and manipulate database record through a graphical user interface (GUI). Different types of information are displayed in an intuitive fashion in user-configurable “tracks”. Galaxy overview and Interface. Getting Data in Galaxy. Analyzing Data in Galaxy . Quality Control. Mapping Data. History and workflow. Galaxy Exercises . (https://. galaxy.bioinfo.ucr.edu. /). NGS Analysis Using Galaxy. and . transcriptomics. Daniel Hurley. What are we going to talk about?. Understanding the core principles and ‘root hypothesis’ of . transcriptomics. Choosing between different . technologies. How to design an experiment. Day 1: Library prep, gel purification: Ligate 3' Adapter: 1.5 hrs, waiting time 45 min; Ligate 5' Adapter: 1.5 hrs, waiting time 45 min; Reverse Transcription: 1h 15 min, waiting time 45 min; Gel puri ORFans. to . “GO”. Genomic sequence of model eukaryote . Saccharomyces cerevisiae . completed in 1996. (12.1 Mb). Despite 16 years of intense research, function of nearly 30% of putative open reading frames (ORFs) remain unknown.. TheXevaUser'sGuide1Introduction TheXevapackageprovidesecientandpowerfulfunctionsforpatient-drivedxenograft(PDX)basedpharmacogenomicdataanalysis[1].2InstallationandSettings Xevarequiresthatseveral Vladimir Benes1 Jonathon Blake1 Ken Doyle21European Molecular Biology Laboratory Genomics Core Facility Heidelberg Germany2Epicentre an Illumina company Madison Wisconsin USA Correspondence should be - Overview -. Why gene expression analysis?. Quantification of mRNA transcript abundance. High specificity, +/- high through-put. Requires sequence knowledge. Considerations. Experimental question. Species limitations . QC. 1. QC summary. 2. QC was performed on all 192 samples focusing on determining failed or outlier. samples. Four samples are recommended for omission from the final analysis. dataset based on evidence of RNA degradation, PCA analysis, and model-based. Vince Buonaccorsi. Juniata College. Cost of sequencing. https://www.genome.gov/about-genomics/fact-sheets/Sequencing-Human-Genome-cost. Next (2. nd. ) Generation Sequencing. How does Illumina sequencing work?. (something always goes wrong). John Hutchinson. Harvard Chan Bioinformatics Core. RNAseq workflow. design experiment. isolate samples. isolate RNA. ribodeplete?. make libraries and barcode samples. sequence.

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