Re: [MUMmer-help] Fwd: Regarding nucmer+mummerplot

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

Hi Lava,
Mummerplot doesn't use a window size, but plots points proportional to the
size of the matches found. Every match in the delta file will be plotted.
Actually, it plots the end points of the match and connects them with a
line. In your case, the matches are relatively small and so you are only
seeing the end points.

Those vertical lines are caused by repeats. If you would like to filter
them out, you can try the 'delta-filter' tool:

> delta-filter -m prefixA.delta > prefixA.m.delta
> mummerplot -p prefixB -png prefixA.m.delta

This should clean up most of the repeats. If you want a 1-to-1 mapping
(e.g. each location on your referenced mapped to only one location on the
query) you can use:

> delta-filter -1 prefixA.delta > prefixA.m.delta
> mummerplot -p prefixB -png prefixA.1.delta

Best,
-Adam


On Sat, Feb 6, 2016 at 7:54 AM, Lavanya Rishishwar <
lav...@gm...> wrote:

> Hi,
>
> To start with, MUMmer is a great package!  Thanks for having such a nice
> manual with it!
>
> I am using nucmer followed by mummerplot to draw alignment plots and I
> have a couple of questions regarding it.
>
> My commands are as follows:
>
> nucmer -p prefixA ref.fasta query.fasta
> mummerplot -p prefixB -png prefixA.delta
>
> This generates me a rather pretty looking plot which is great (please see
> the attached file).  My questions are:
> 1) How big is the default window size for each plotted point?  If there is
> a variation in the size, is there a way I can figure out what the size is?
> 2) I am getting a set of vertical lines in all my dot plot at the same
> loci against a specific reference that I have.  This is possible if the
> window size is really small but then I should be seeing a lot of noise
> which is also not the case.  Is my interpretation correct? If yes, how can
> I eliminate these vertical lines (in the sense of controlling the
> parameters with nucmer/mummerplot)?  If no, any ideas of what this could be?
>
> Your time is much appreciated!
>
> Thanks,
> Lava
>
>
>
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