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18 lines
570 B
Bash
18 lines
570 B
Bash
#!/bin/bash
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# My first script
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if [ $# -eq 1 ]
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then
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echo "../minimap2/minimap2 -ax asm20 -t 32 ../minimap2/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz "$1" >"$1".sam"
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../minimap2/minimap2 -ax asm20 -t 32 ../minimap2/Homo_sapiens.GRCh38.dna.primary_assembly.fa $1 >$1.sam
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echo "samtools view -Sb "$1".sam >"$1".bam"
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samtools view -Sb $1.sam >$1.bam
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echo "samtools sort "$1".bam sort_"$1
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samtools sort $1.bam sort_$1
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echo "rm sort_"$1".bam.bai"
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rm sort_$1.bam.bai
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echo "samtools index sort_"$1".bam"
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samtools index sort_$1.bam
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else
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echo "debug_assembly.sh intput.fa"
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fi
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