（Transcriptome study based on RNA-seq data）第二代RNA-Seq数据分析理论及上机.pptxVIP

Transcriptome study based on RNA-seq data第二代RNA-Seq数据分析理论及上机;OUTLINE;转录组（transcriptome）;;随着第二代测序技术的迅猛发展，其高通量、快速、低成本的特点成为越来越多的生物学研究者在解决生物学问题时的首选，尤其在转录组测序(RNA-seq)方面更显示出极大的潜力。尤其相对于真核生物全基因组测序来说，转录组测序得到的序列不含有内含子及其它非编码序列，因此转录组 测序有着无可比拟的高性价比优势。 目前转录组测序及分析技术 可以解决 转录图谱绘制 基因表达谱的构建、新基因的深度发掘、低丰度转录本的发现、代谢途径确定、 RNA Variation cSNP的鉴定、可变剪接的研究、融合基因鉴定、RNA-editing ;mRNA-seq technology;mRNA-seq data analysis strategy;Overview of RNA-seq transcriptome data analysis;;RawReads #;Mapping and mapping result assessment;Annotation and assessment;Quantification of gene expression level;(1)Calculate express cutoff;Quantification of gene expression level;Pearson correlation analysis between replicate ;Detection of differentially expressed genes ;KEGG pathway annotation and enrichment analysis;Map;Summary;OUTLINE;High-performance transcriptome and small RNA data analysis pipeline; ;Quality distribution result ;miRNA Analysis Results;累计独立IP数;OUTLINE;Advanced topics in study;Clustering;Hierarchical clustering;模糊聚类 算法：FCM 参数： c = 16, m = 1.25 样本： 3000 genes 17 time points;应用举例（一）;应用举例（二）;应用举例（三）;(2) Co-expression network;Using Graphviz ;应用举例（四）;应用举例（五）;(3) Alternative splicing ;(1) Isoform type;(2) Differentially Isoform expressed in genes;(3) Tissue-specific isoform;(5) Expressed transcript comparison ;应用举例（六）;Fuse Gene trans-splicing chromosome recombination ?? Cancer-related genes In plant ??;OUTLINE;Mapping and Assembly tools BWA - BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (targe), such as the human reference genome SeqMap - A Tool For Mapping Millions Of Short Sequences To The Genome.MAQ - stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. ERANGE - Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq Cufflinks - assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.iAssembler – a stand