Convert from bowtie to sam

[tdoniger]

Hi,

I used samtools- bowtie2sam.pl to convert a bowtie file to a sam file. Later, I noticed that some of the alignments were missing in the sam file. Is this expected? Is there another bowtie to sam converter that does not reduce the data? Is it best to choose the sam option from bowtie?

Much Thanks,
Tirza Doniger
Bioinformatics Unit
Bar Ilan University

[colindaven]

Yep, I would choose the SAM option from Bowtie. It has worked consistently well for me

[NicoBxl]

from the bowtie tutorial ( http://bowtie-bio.sourceforge.net/tutorial.shtml )

Finding variations with SAMtools

SAMtools is a suite of tools for storing, manipulating, and analyzing alignments such as those output by Bowtie. SAMtools understands alignments in either of two complementary formats: the human-readable SAM format, or the binary BAM format. Because Bowtie can output SAM (using the -S/--sam option), and SAM can can be converted to BAM using SAMtools, Bowtie users can make full use of the analyses implemented in SAMtools, or in any other tools supporting SAM or BAM.
We will use SAMtools to find SNPs in a set of simulated reads included with Bowtie. The reads cover the first 10,000 bases of the pre-built E. coli genome and contain 10 SNPs throughout. First, we run bowtie to align the reads, being sure to specify the -S option. We also specify an output file that we will use as input for the next step (though pipes can be used to accomplish the same thing without the intermediate file):

bowtie -S e_coli reads/e_coli_10000snp.fq ec_snp.sam

Next, we convert the SAM file to BAM in preparation for sorting. We assume that SAMtools is installed and that the samtools binary is accessible in the PATH.

samtools view -bS -o ec_snp.bam ec_snp.sam

Next, we sort the BAM file, in preparation for SNP calling:

samtools sort ec_snp.bam ec_snp.sorted

[tdoniger]

Thank you.

What concerns me is that some of the alignments returned in the original bowtie file disappeared when I ran bowtie2sam.pl

If I understand correctly now---the script bowtie2sam.pl which comes as part of the samtools package only takes the best hit for each read. However, I had run bowtie with the parameter to report all possible alignments.

I wanted to know if running bowtie with the "SAM" option will exhibit the same behavior as the script bowtie2sam.pl

Thanks
Tirza

[Nick]

allbowtie2sam.pl

I came across this thread with the same issue. As you said bowtie2sam.pl only takes the best read. That is much harder to do than just converting all the hits. I edited the file to print all the reads in a bowtie file to .sam. Although as was said before it's a much better idea to just use the sam output option as that gives you a header that is missing with this conversion. However sometimes you just need to convert something that was already done.

[yuelics]

I have a related question. How can I make bowtie to output both sam and bowtie format without running it twice with two different output options? Some downstream programs need bowtie format, but some need sam/bam.

Thanks in advance for any reply!