bowtie map to BED conversions

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bowtie map to BED conversions

Ry4an Brase-3
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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Re: bowtie map to BED conversions

Anton Nekrutenko
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
> _______________________________________________
> galaxy-dev mailing list
> [hidden email]
> http://lists.bx.psu.edu/listinfo/galaxy-dev


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