Ry4an:

SAM output generated with bowtie can be converted into BED-like format with 
NGS: Samtools -> Convert SAM to interval. However, it is not sorted.

Tx,

anton



On Jan 6, 2011, at 6:12 PM, Ry4an Brase wrote:

> I've got a user request for a converter from bowtie's map output to BED
> format, and looking at the provided script it's mostly just an
> application of cut(1) and sort(1).
> 
> Is this something Galaxy already does through some mechanism we're not
> finding or is this 3 line conversion script something I should be
> adding and submitting back?
> 
> Thanks,
> 
> -- 
> Ry4an Brase                                         612-626-6575
> Software Developer                                  Application Development
> University of Minnesota Supercomputing Institute    http://www.msi.umn.edu
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> galaxy-dev@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev


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