Dear all
How can i pipe the following bowtie's commands so the terminal on mac would run them all at once
Many thanks for your help.
How can i pipe the following bowtie's commands so the terminal on mac would run them all at once
bowtie-build mainseq.fasta build
bowtie -S build -f -I 20 -X 7500 -a -m 1 -v 3 --rf -1 reads_1.fasta -2 reads_2.fasta aligned.sam
samtools view -bS aligned.bam aligned.sam
samtolls sort aligned.bam aligned.sorted
samtools index aligned.sorted.bam
bowtie -S build -f -I 20 -X 7500 -a -m 1 -v 3 --rf -1 reads_1.fasta -2 reads_2.fasta aligned.sam
samtools view -bS aligned.bam aligned.sam
samtolls sort aligned.bam aligned.sorted
samtools index aligned.sorted.bam
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