make reference index
/home/galaxy/galaxy-dist/bin/bwa index -p 454.bwa.index -a bwtsw assembly1/454AllContigs.fna
paired-end alignment
/home/galaxy/galaxy-dist/bin/bwa aln 454.bwa.index -I denovo/Gal_trim1.fastq > Gal_trim1.bwa.aln.sai
/home/galaxy/galaxy-dist/bin/bwa aln 454.bwa.index -I denovo/Gal_trim2.fastq > Gal_trim2.bwa.aln.sai
/home/galaxy/galaxy-dist/bin/bwa sampe 454.bwa.index Gal_trim1.bwa.aln.sai Gal_trim2.bwa.aln.sai denovo/Gal_trim1.fastq denovo/Gal_trim2.fastq > Gal.bwa.sam
converts sam to bam
/home/galaxy/galaxy-dist/bin/samtools view -bT assembly1/454AllContigs.fna Gal.bwa.sam > Gal.bwa.bam
/home/galaxy/galaxy-dist/bin/samtools sort Gal.bwa.bam Gal.bwa.sorted.bam
/home/galaxy/galaxy-dist/bin/samtools index Gal.bwa.sorted.bam Gal.bwa.sorted.bai
/home/galaxy/galaxy-dist/bin/samtools flagstat Gal.bwa.sorted.bam
'Bioinformatics' 카테고리의 다른 글
| how to blast to nr database (0) | 2012.04.27 |
|---|---|
| how to make reverse complement of sequence in shell (0) | 2012.03.05 |
| Promoter 지역에서 특정 motif 찾기 (0) | 2012.02.20 |
| ABySS 사용시 주의점 (0) | 2012.02.09 |
| xys 링크파일만들기 (0) | 2011.12.14 |