Re: [MUMmer-help] mapview question

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

Hello Erica,
Unfortunately the developer of MapView is no longer with our group, and the
tool is no longer supported.

On the other hand, mummerplot is supported, and can handle multiple
sequences. Simply providing mummerplot with the .delta file should be
sufficient.

> mummerplot --layout --large out.delta

Best,
Adam Phillippy

On Fri, Jun 13, 2008 at 1:25 PM, Lasek-Nesselquist, Erica <
Eri...@br...> wrote:

> Dear support staff,
>  I have used nucmer to generate a .delta file of two draft genomes (both
> assemblies contain multiple contigs in fasta format).  As per the manual
> directions, I used this .delta file to create a coord file using the
> show-coords command, which should then allow me to generate a graphical
> presentation of the data using mapview.  However, I am having trouble using
> mapview.  When I use the mapview command and redirect the standout to a
> file, the file simply contains a list of contigs with lengths in the next
> column. If I attempt to specify that I would like the file in a pdf readable
> format, it will not recognize the option.  Is there a key step in the
> process I am missing?
>
> Also, the options -R and -Q are not recognized in mummerplot, even thought
> they are listed as ways to compare files that contain multiple fasta
> entries.  Are these options available?  Is there another way to generate the
> output from mummerplot using two files that contain multiple contigs?
>
> Thank you,
> Erica Lasek-Nesselquist
>
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