bam output file to psl file

fahim

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Join Date: Oct 2010

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#1

bam output file to psl file

12-26-2010, 10:23 AM

Hi
I am doing short read alignment using bwa algorithm. I am able to convert the alignment output to .bam file.
Now, I want to see the alignments and how a read maps to the genome. In case of BLAT or other aligners such as bowtie, gives an output which contains information such as "readName, referenceChromosome, tStart, tEnd, qSize, etc ..etc..". I want the output in similar format.
Is there a way/command/software to do that through samtools.
Thanks in advance.
Fahim

Last edited by fahim; 12-26-2010, 10:25 AM. Reason: typo
Tags: bwa, sam
drio

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Join Date: Oct 2008

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#2

12-26-2010, 01:27 PM

I suggest you spend some time getting yourself familiar with the format since (S|B)AM is the standard to store and represent alignments. It is here to stay.

Those specific fields you are looking for you can find in your BAM output from BWA. Take a look to the specification. Pay particular attention to section 1.4.

Furthermore, most of the downstream tools you may want to use are going to require alignments in (S|B)AM.

-drd
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