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

[Sanjit S. B. <san...@gm...>]

Hey!

I have a 30Mb scaffold that was assembled using optical maps. I would like
to align it to a 3Gb long reference assembly. Given the method through
which this scaffold was constructed, it should align to a region in the
reference, roughly the same size as itself.

I am currently running nucmer with the -c 100 flag, and I get a very large
number of fragmented alignments, the longest of which is under 1Mb. Is
there any way I can alter the flags to get a larger, less fragmented
alignment, for this particular case?

Any suggestions are appreciated. Thanks!

On Tue, Apr 21, 2015 at 10:25 AM, Adam Phillippy <aph...@gm...>
wrote:

> 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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