短序列比对练习

生信喵

一、比对练习

1. mkdir 52.bwa
   
2. #1 bwa比对
   
3. #建立索引
   
4. ln -s /share/home/xiehs/05.assembly/data/MGH78578.fasta .
   
5. 
   
6. #bwa比对
   
7. 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
   
8. 
   
9. #bwa-mem2比对
   
10. bwa-mem2 index MGH78578.fasta
    
11. 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
    
12. 
    
13. #bwa+samtools一条命令
    
14. 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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1. #拟南芥比对
   
2. ln -s /share/home/xiehs/05.assembly/ninanjie/tair10.fna
   
3. bwa-mem2 index tair10.fna
   
4. 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。

1. #bowtie2与hisat2比较
   
2. ln -s /share/home/xiehs/07.aligment/data/chrX.fa .
   
3. bowtie2-build chrX.fa chrX
   
4. 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
   
5. 
   
6. hisat2-build chrX.fa chrX
   
7. 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
   
8. 
   
9. bowtie2.sam 680M
   
10. 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。