数据处理及组装-杭州.pdfVIP

测序数据的处理 测序数据的处理 倪培相 倪培相 nipx@genomics.org.cn nipx@genomics.org.cn Total strategy of shotgun sequencing and assembly 测序技术中的核心技术 测序技术中的核心技术 Sanger双脱氧终止法 Sanger双脱氧终止法 PCR技术 PCR技术 对L-W理论曲线的讨论 对L-W理论曲线的讨论 设： G = haploid genome length in bp; L = length of clone insert in bp; N = number of clones fingerprinted; α = N / G = probability per base of starting a number clone; T = amount of overlap in base pairs needed to detect overlap; θ = T / L; overlap in base pairs needed to detect overlap; c = redundancy of coverage = LN/G . L ⋅N c G Proposition 1. Let θbe the fraction of which two clones mucst share in order that the overlap ? detectable given the fingerprinted scheme, let N be the number of clones fingerprinted, and let c be the redundancy of coverage. Also, let T σ 1− 1− θ L 1. The expected number of apparent islands is Ne−cσ 2. The expected number of apparent islands composisting ofj clones is (j ≥1) Ne−2cσ(1−e−cσ)j −1 3. The expected number of apparent islands composisting of at least two clones is Ne−cσ−Ne−2cσ Contig 个数 Contig 个数 Contig 覆盖度 Contig 覆盖度 与实际曲线的比较 与实际曲线的比较 常用数据处理软件的使用 常用数据处理软件的使用 • phred • phred • phd2fasta • phd2fasta • cross_match • cross_match • phrap • phrap • consed • consed 一、phred 一、phred • 功能：从上游得到的峰图文件中读出碱基生成phd文 • 功能：从上游得到的峰图文件中读出碱基生成phd文 件。 件。 • 前提：setenv PHRED_PRAMETER_FILE • 前提：setenv PHRED_PRAMETER_FILE /usr/local/genome/bin/lib/phredpar.dat /usr/local/genome/bin/lib/phredpar.dat • 基本命令： phred -id chromat_dir/ -pd phd_dir/ - • 基本命令： phred -id