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