[Bioc-sig-seq] use pipes to map reads with bowtie and convert to BAM

[James W. MacDonald]

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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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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