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

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

Thank you very much Adam! This was exactly what I was trying to do!

On Sun, Feb 7, 2016 at 4:50 PM, Adam Phillippy <aph...@gm...> wrote:

> 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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>