bwa比对

构建索引

[u20111230014@cpu10 GRCm39]$ bwa index bwa_index/GRCm39.fa

mem比对
mem Usage: bwa mem [options] ref.fa reads.fq [mates.fq]

操作路径
[u20111230014@cpu10 GRCm39]$ pwd
/home/u20111230014/workspace/genome/GRCm39
[u20111230014@cpu10 GRCm39]$ ll
total 1141720
drwxrwxr-x 3 u20111230014 u20111230014      4096 Feb 20 20:34 bowtie2_index
drwxrwxr-x 2 u20111230014 u20111230014      4096 Feb 20 20:48 bwa_index
-rw-r--r-- 1 u20111230014 u20111230014       602 Feb 20 20:53 bwa.slurm
lrwxrwxrwx 1 u20111230014 u20111230014        53 Feb 20 19:50 DPP-0_clean.fq -> /home/u20111230014/workspace/Cleandata/DPP-0_clean.fq
-rw-rw-r-- 1 u20111230014 u20111230014         0 Feb 20 20:49 DPP-0.sam
lrwxrwxrwx 1 u20111230014 u20111230014        53 Feb 20 19:50 DPP-1_clean.fq -> /home/u20111230014/workspace/Cleandata/DPP-1_clean.fq
lrwxrwxrwx 1 u20111230014 u20111230014        53 Feb 20 20:53 DPP-2_clean.fq -> /home/u20111230014/workspace/Cleandata/DPP-2_clean.fq
lrwxrwxrwx 1 u20111230014 u20111230014        53 Feb 20 20:54 DPP-3_clean.fq -> /home/u20111230014/workspace/Cleandata/DPP-3_clean.fq
lrwxrwxrwx 1 u20111230014 u20111230014        53 Feb 20 20:54 DPP-4_clean.fq -> /home/u20111230014/workspace/Cleandata/DPP-4_clean.fq
lrwxrwxrwx 1 u20111230014 u20111230014        53 Feb 20 20:54 DPP-5_clean.fq -> /home/u20111230014/workspace/Cleandata/DPP-5_clean.fq
lrwxrwxrwx 1 u20111230014 u20111230014        47 Feb 20 20:11 go_FPKM_PE.sh -> /home/public/software/wfz_scripts/go_FPKM_PE.sh
lrwxrwxrwx 1 u20111230014 u20111230014        47 Feb 20 20:09 go_FPKM_SE.sh -> /home/public/software/wfz_scripts/go_FPKM_SE.sh
-rw-r--r-- 1 u20111230014 u20111230014 310889939 Feb 18 14:31 GRCm39.gff3
-rw-r--r-- 1 u20111230014 u20111230014 858193862 Feb 18 14:30 GRCm39.gtf

具体的slurm 文件内容

[u20111230014@cpu10 GRCm39]$ more bwa.slurm 
#!/bin/bash
#SBATCH -J Job.SRR87   
#SBATCH -p dna             
#SBATCH -N 1  
#SBATCH --mem=50G               
#SBATCH --cpus-per-task=25    
#SBATCH -t 1-10:00:00        
#SBATCH -o Out.SRR87   
#SBATCH --mail-user=xxx@qq.com

bwa mem -t 24 bwa_index/GRCm39.fa DPP-0_clean.fq > DPP-0.sam

sbatch bwa.slurm即可！