On Fri, Aug 12, 2011 at 3:21 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> On the bright side, convert to BED seems to work.

Well, sort of. After converting that GFF3 file into BED, the strand column
isn't set in the metadata. That seems important!

Also a point of clarification, I had the wrong URL for the FASTA file.

This is the whole genome, although to actually proceed with this
example, the sequence must be renamed to just NC_005213.1
rather than the NCBI's gi|38349555|ref|NC_005213.1| in order
to match the naming in the GFF file.

The file I linked to in the earlier email is what I am trying to reproduce,

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