短序列比对练习

一、比对练习

mkdir 52.bwa

#1 bwa比对

#建立索引

ln -s /share/home/xiehs/05.assembly/data/MGH78578.fasta .

#bwa比对

bwa mem MGH78578.fasta /share/home/xiehs/05.assembly/data/illumina_1.fastq.gz /share/home/xiehs/05.assembly/data/illumina_2.fastq.gz >MGH78578.sam

#bwa-mem2比对

bwa-mem2 index MGH78578.fasta

time bwa-mem2 mem MGH78578.fasta /share/home/xiehs/05.assembly/data/illumina_1.fastq.gz /share/home/xiehs/05.assembly/data/illumina_2.fastq.gz >MGH78578.sam

#bwa+samtools一条命令

bwa-mem2 mem -t 12 MGH78578.fasta /share/home/xiehs/05.assembly/data/illumina_1.fastq.gz /share/home/xiehs/05.assembly/data/illumina_2.fastq.gz | samtools sort -O bam - >MGH78578.sorted.bam

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#拟南芥比对

ln -s /share/home/xiehs/05.assembly/ninanjie/tair10.fna

bwa-mem2 index tair10.fna

bwa-mem2 mem -t 12 tair10.fna /share/home/xiehs/05.assembly/ninanjie/illumina/il_1.fq.gz /share/home/xiehs/05.assembly/ninanjie/illumina/il_2.fq.gz >tair10.sam 2>bwa.log

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二、split比对

    针对人基因组RNA-Seq，read跨越外显子，此时要使用支持切除read的软件，例如tophat2，升级的hisat2.而bowtie2则不行。下面我们可以来对比下。

#bowtie2与hisat2比较

ln -s /share/home/xiehs/07.aligment/data/chrX.fa .

bowtie2-build chrX.fa chrX

bowtie2 -x chrX -p 12 -1 /share/home/xiehs/07.aligment/data/ERR188044_chrX_1.fastq.gz -2 /share/home/xiehs/07.aligment/data/ERR188044_chrX_2.fastq.gz >bowtie2.sam 2> bowtie2.log

hisat2-build chrX.fa chrX

hisat2 -p 12 --dta -x chrX -1 /share/home/xiehs/07.aligment/data/ERR188044_chrX_1.fastq.gz -2 /share/home/xiehs/07.aligment/data/ERR188044_chrX_2.fastq.gz -S hisat2.sam 2> hisat2.log

bowtie2.sam 680M

hisat2.sam 737M

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   hisat2支持split比对，可以看到文件大小比bowtie2的结果更多了。

    其他的软件还有soap软件，但是很久没有更新了。STAR也是做RNA-Seq的，参数比较多。