生成 bam

生信喵

1. #fastqc质控
   
2. mkdir 20.human;cd 20.human
   
3. mkdir ref;cd ref
   
4. axel -n 100 https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta
   
5. #建立bwa-mem2索引
   
6. bwa-mem2 index -p Homo_sapiens_assembly38.fasta Homo_sapiens_assembly38.fasta
   
7. 
   
8. vi reads.list
   
9. /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L001_R1_001.fastq.gz /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L001_R2_001.fastq.gz
   
10. /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L001_R1_002.fastq.gz /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L001_R2_002.fastq.gz
    
11. /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L001_R1_003.fastq.gz /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L001_R2_003.fastq.gz
    
12. /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L001_R1_004.fastq.gz /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L001_R2_004.fastq.gz
    
13. /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L002_R1_001.fastq.gz /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L002_R2_001.fastq.gz
    
14. /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L002_R1_002.fastq.gz /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L002_R2_002.fastq.gz
    
15. /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L002_R1_003.fastq.gz /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L002_R2_003.fastq.gz
    
16. /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L002_R1_004.fastq.gz /share/home/xiehs/data/Project_RM8398/Sample_U0a/U0a_CGATGT_L002_R2_004.fastq.gz
    
17. 
    
18. mkdir qc
    
19. nohup fastqc -f fastq -o qc -t 16 /share/home/xiehs/data/Project_RM8398/Sample_U0a/*.fastq.gz &
    
20. multiqc qc -o multiqc
    
21. #fastp过滤
    
22. cat reads.list | while read {i,j};do echo fastp -i ${i} -I ${j} -o ${i%*.fastq.gz}_clean.fastq.gz -O ${j%*.fastq.gz}_clean.fastq.gz -z 4 -q 20 -u 40 -n 10 ;done;
    
23. sed -i 's#/share/home/xiehs/data/Project_RM8398/Sample_U0a/##3' fastp.sh
    
24. sed -i 's#/share/home/xiehs/data/Project_RM8398/Sample_U0a/##3' fastp.sh
    
25. bsub -q fat -n 10 -o %J.log -e %J.err sh fastp.sh
    
26. 
    
27. vi clean.list
    
28. ls *.gz | xargs -n 2 #后在修改
    
29. clean/U0a_CGATGT_L001_R1_001_clean.fastq.gz clean/U0a_CGATGT_L001_R2_001_clean.fastq.gz
    
30. clean/U0a_CGATGT_L001_R1_002_clean.fastq.gz clean/U0a_CGATGT_L001_R2_002_clean.fastq.gz
    
31. clean/U0a_CGATGT_L001_R1_003_clean.fastq.gz clean/U0a_CGATGT_L001_R2_003_clean.fastq.gz
    
32. clean/U0a_CGATGT_L001_R1_004_clean.fastq.gz clean/U0a_CGATGT_L001_R2_004_clean.fastq.gz
    
33. clean/U0a_CGATGT_L002_R1_001_clean.fastq.gz clean/U0a_CGATGT_L002_R2_001_clean.fastq.gz
    
34. clean/U0a_CGATGT_L002_R1_002_clean.fastq.gz clean/U0a_CGATGT_L002_R2_002_clean.fastq.gz
    
35. clean/U0a_CGATGT_L002_R1_003_clean.fastq.gz clean/U0a_CGATGT_L002_R2_003_clean.fastq.gz
    
36. clean/U0a_CGATGT_L002_R1_004_clean.fastq.gz clean/U0a_CGATGT_L002_R2_004_clean.fastq.gz
    
37. 
    
38. #bwa-mem2比对
    
39. mv filter clean
    
40. cat clean.list | while read {i,j};do echo bwa-mem2 mem -t 4 -o ${i%*_clean.fastq.gz}.sam -R \'@RG\\tID:A1\\tPL:illumina\\tSM:human\' /share/home/xiehs/20.human/ref/Homo_sapiens_assembly38.fasta ${i} ${j};done;
    
41. bsub -q fat -n 4 -o %J.log -e %J.err sh bwa.sh

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