Hi Nick,
As I recall, show-tiling only uses sequences directly from the contigs and
does not try and compute any kind of consensus when two contigs overlap, so
I can't think of any reasonable explanation for what you are seeing. If your
dataset is not too big, and you would like me to take a look, please forward
it along.
On another note, I've never been happy with show-tiling's performance and
have been gradually replacing it with the program 'delta-filter'. If you run
'delta-filter -q out.delta > new.delta' you will get a filtered alignment
file that only reports the best matches for each contig to the reference (
i.e. each base of the contig is mapped to one location on the reference).
This program is superior because it allows contigs to be broken and aligned
to different parts of the reference if necessary, but there is no way to
turn this into a pseudo-molecule, yet.
Best,
Adam Phillippy
On 3/14/07, Nick Peters <np1@...> wrote:
>
> Hi,
>
> I'm using show-tiling to create a pseudo-molecule and I'm running into
> problems when trying to mark up the locations of the original contigs on
> it.
>
> Is there a good explanation of how the pseudo-molecule is built
> somewhere or can someone please explain? There are big chunks of the
> pseudo-molecule that don't perfectly match to any of my original contigs
> so it is obviously doing something rather cleverer than simply laying
> out the contigs in the order of the tiling path padded with Ns.
>
> Apologies if this is documented somewhere I haven't spotted.
>
> Thanks
>
> Nick
>
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