How do I use pipes to map reads with bowtie and convert to BAM without the
intermediate files?
>From the following steps, I am interested only in 'reads_sorted.bam' file:
#run bowtie to align the reads
bowtie -S ebwt reads.fastq reads.sam
#convert the SAM file to BAM
samtools view -bS -o reads.bam reads.sam
#sort the alignment
samtools sort reads.bam reads_sorted
#index the alignment
samtools index reads_sorted.bam
Thank you
Joseph Dhahbi
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