Re: [MUMmer-help] Show-tiling: Switching the Reference and Query in a delta file

[Adam P. <aph...@gm...>]

Hi Sanjit,
There is no easy way to switch the reference and query once the alignment
is computed.

What do you intend to use show-tiling for? The 'delta-filter' program can
be more flexible and useful for some tasks. If you run 'delta-filter -r' it
will select the best alignments for each of your smaller reference
sequences mapped to the larger query. If you run 'delta-filter -q' it will
select the best alignment covering each region of your large query, which
will (in effect) be similar to a tiling path of the best reference
alignments across the query.

Hope this helps,
-Adam


On Tue, Apr 14, 2015 at 9:45 PM, Sanjit Singh Batra <san...@gm...>
wrote:

> Hey!
>
> As mentioned in the manual, I switched the reference and the query while
> using nucmer, since the reference was very large, and much larger than the
> query. Now, I would like to run the show-tiling module on the resulting
> delta file(This feature was the primary reason I started using mummer).
> However, since the reference and query are switched, it tiles the reference
> chromosomes over contigs, which is not what is desired.
>
> So, is there a script that can switch the reference and the query in a
> delta file?
>
> Any suggestions are greatly appreciated. Thanks for your time!
>
>
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