32 lines
701 B
Bash
32 lines
701 B
Bash
#!/bin/bash
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mkdir results
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# Question 1
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soft/bowtie2 --end-to-end --fast -x databases/all_genome.fasta -1 EchE_R1.fastq.gz -2 EchE_R2.fastq.gz -S results/alignment.sam
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# Question 2
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# a
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samtools view -b results/alignment.sam
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# b
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samtools sort -@ 4 results/alignment.bam -o results/alignment.sorted.bam
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# c
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samtools index results/alignment.sorted.bam
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# d
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samtools idxstats -@ 4 results/alignment.sorted.bam > results/alignment.idx
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# f
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grep ">" databases/all_genome.fasta|cut -f 2 -d ">" > results/association.tsv
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# Question 3
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soft/megahit --k-list 21 --mem-flag 0 -1 EchE_R1.fastq.gz -2 EchE_R2.fastq.gz -o contigs
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# Question 4
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soft/prodigal -i contigs/final.contigs.fa -f fasta > genes.fna
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