基因组文件处理 | Sly Li

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https://slyli.cn/posts/2021-03-002.html

靖康耻，犹未雪。臣子恨，何时灭。驾长车，踏破贺兰山缺。壮志饥餐胡虏肉，笑谈渴饮匈奴血。待从头、收拾旧山河，朝天阙。

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bwa index 02.genome.fa bwa mem -t 14 02.genome.fa ~/data/JY_1_Q20L50_1.fastq.gz ~/data/JY_1_Q20L50_2.fastq.gz > 2_hiseq_full_align.sam samtools view -@ 14 -b -S 2_hiseq_full_align.sam > 2_hiseq_full_align.bam samtools sort -@ 14 2_hiseq_full_align.bam -o 2_hiseq_full_align.sort.bam samtools index -@ 14 2_hiseq_full_align.sort.bam

rm 2_hiseq_full_align.sam

minimap2 -t 14 -ax map-pb 02.genome.fa ~/data/2.JY/m54191_reads.fastq.gz > 2_pacbio_full_align.sam samtools view -@ 14 -b -S 2_pacbio_full_align.sam > 2_pacbio_full_align.bam samtools sort -@ 14 2_pacbio_full_align.bam -o 2_pacbio_full_align.sort.bam samtools index -@ 14 2_pacbio_full_align.sort.bam

rm 2_pacbio_full_align.sam

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samtools view -b -F 4 2_pacbio_full_align.sort.bam chr13:39648817-39928014 >pacbio_rela_reads.bam