Hi Joseph,
I think you want to ask questions about samtools on the samtools listserv!
But this page might be helpful for you:
http://sourceforge.net/apps/mediawiki/samtools/index.php?title=SAM_protocol#Perform_alignment
Best,
Jim
joseph wrote:
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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