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 galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev