序列比对生物信息学进展实验课3.ppt

/angus/tutorials-2012/bwa_tutorial.html * 生物信息学进展 （3）序列比对 测序数据分析流程 * 1.数据预处理 数据文件 FastQ文件 mapping file 原始数据 FastQ文件 2.序列比对 初步结果 3.数据分析 进一步的结果 4. GO analysis ChIP-Seq RNA-Seq ChIA-PET 。。。 序列比对问题 将测序数据比对到参考基因组 最早的序列比对，是两个基因序列之间的比对 * 原始数据 – FastQ文件 FastQ文件 1. A line starting with @ containing the sequence identifier 2. real sequence 3. a line starting with + after which the sequence identifier is optional 4. encodes the quality values for the sequence in Line 2, and must contain the same number of symbols as letters in the sequence * 以ChIP-Seq数据为例 下载ChIP-Seq数据 [bio2014@node8 Arabidopsis_thaliana]$ nohup wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR651/SRR651185/SRR651185.fastq.gz * 参考基因组 拟南芥 /pub/plants/release-21/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.21.dna.genome.fa.gz 水稻 /pub/plants/release-21/fasta/oryza_sativa/dna/Oryza_sativa.IRGSP-1.0.21.dna.genome.fa.gz 人类 /goldenPath/hg19/bigZips/chromFa.tar.gz 小鼠 /goldenPath/mm10/bigZips/chromFa.tar.gz 果蝇 /genomes/Drosophila_melanogaster/dmel_r5.55_FB2014_01/fasta/dmel-all-chromosome-r5.55.fasta.gz 下载参考基因组 wget 所需参考基因组 * Software for NGS mapping BWA Heng Lis BWT Alignment program - a progression from Maq. BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence. C++ source. Bowtie/Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. ELAND - Efficient Large-Scale Alignment of Nucleotide Databases Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine SOAP - SOAP (Short Oligonucleotide Alignment Program) / A program for efficient gapped and ungapped alignment of short oligonucleotides onto referen