第二代测序数据原理教材.pptVIP

问题出发 正常样本与异常样本，如肿瘤等； 药物处理前后样本状态变化，如尼古丁刺激前后； 发育不同阶段的样本改变 ............. 第二代测序数据分析原理 徐汪节 概要 主要的测序平台 基因组分析原理 转录组分析原理 分析策略的选择 Second generation sequence Roche 454 Metagenomics De novo sequencing RNA-seq illumia Solexa De novo sequencing Re-sequencing RNA-seq (ChromatinImmunoprecipitation，ChIP) Meth-seq ABI SOLiD Re-sequencing ChIP-seq RNA-seq Experiments DNA-seq: de novo, resequencing RNA-seq:mRNA, ncRNA, smRNA... ChIP-seq: Chromatin ImmunoPrecipitation Methyl-seq: methylated DNA (epigenome) 主要的测序平台 基因组分析原理 转录组分析原理 分析策略的选择 Sequencing Glossary Reads. A collection of clones that over-sample the target genome. Pair-end reads.Sequence reads derived from both ends of a sequencing-library clone. Mate-pair reads.Sequence reads derived from both ends of a mate-pair library clone which insert size is usually1kb. Insert size. The size of the clone-insert from which a clone-end pair is taken. Contig. The result of joining an overlapping collection of sequence reads. Scaffold. The result of connectiing non-overlapping contiges by using pir-end reads. N50 size. As applied to contigs or scaffolds, that size above which 50% od the assembled 全基因组de nove分析工具 分析所需工具 Bowtie software -/index.shtml/ SAM tools -/ TopHat softare -/ Cufflinks software -http://C/ CummeRbund software -/cummeRbund/ 外显子组分析工具 主要的测序平台 基因组分析原理 转录组分析原理 分析策略的选择 常规分析 Transcripts quantification Splicing sites discovery and quantification Gene discovery SNP/INDEL detection Allele specific expression UniGene拼接 目的：将预处理后reads进行拼接，得到拼接结果。  原理： 应用 de Bruijn graph path 算法对reads进行denovo拼接；对上一步的拼接结果，再用Hamilton Path算法拼接。  结果：UniGene序列，UniGene统计信息，序列长度分布图 3. 数据库注释 目的：对拼接得到的UniGene进行功能注释