Bioinformatics

usage bwa using paired-end reads

홍조 2012. 4. 5. 15:47

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 

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