[MUMmer-help] Fwd: Regarding nucmer+mummerplot

[Lavanya R. <lav...@gm...>]

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