Re: [MUMmer-help] NUCmer + mummerplot to compare two draft assemblies

[Qihua L. <qli...@uc...>]

Hi Adam and other MUMmer support team,

I attached a screenshot of mummerplot output. There are some thick lines and some thin ones. I am wondering if those thick lines are clusters of start and end of each hit (which are represented by dots) and thin lines are the long alignments which are represented by lines. 

Besides of ps output format, could it be other higher resolution format like svg, which I could zoom it to see more details of whether are are gaps between some alignments?

Thank you
Qihua



> On Dec 11, 2017, at 1:46 PM, Adam Phillippy <aph...@gm...> wrote:
> 
> Not unusual. If you zoom in on the interactive plot (right mouse button) you should be able to see what's happening. Likely to be small, in-place inversions w/in contigs or at the ends of contigs.
> 
> On Mon, Dec 11, 2017 at 4:43 PM, Qihua Liang <qli...@uc... <mailto:qli...@uc...>> wrote:
> Hi Adam,
> 
> What about blue plots aligning on the diagonal? I attached a figure and it looks like blue and red are both aligning along the diagonal. I think the blue one should from the other diagonal?
> 
> Thank you
> Qihua
> 
> <PastedGraphic-1.png>
> 
> 
>> On Dec 11, 2017, at 12:39 PM, Adam Phillippy <aph...@gm... <mailto:aph...@gm...>> wrote:
>> 
>> Yes, red are forward-strand matches and blue are reverse. Large stretches of blue would indicate inversions, though smaller ones may just be repetitive matches.
>> 
>> Best,
>> -Adam
>> 
>> On Mon, Dec 11, 2017 at 3:29 PM, Qihua Liang <qli...@uc... <mailto:qli...@uc...>> wrote:
>> Hi Adam,
>> 
>> Thank you for your advice on -l. It works great with generating the diagonal plot.
>> 
>> But it is confusing that the diagonal plot seems to have both red and blue color on it. I think it means both forward and reverse matches on the same position, but why would that happen?
>> 
>> Thanks
>> Qihua
>> 
>>> On Nov 29, 2017, at 12:34 PM, Adam Phillippy <aph...@gm... <mailto:aph...@gm...>> wrote:
>>> 
>>> Hi Qihua,
>>> Try adding the --layout or --fat options and mummerplot will arrange and orient the contigs to make things look better.
>>> 
>>> Best,
>>> -Adam
>>> 
>>> On Mon, Nov 27, 2017 at 4:28 AM, Qihua Liang <qli...@uc... <mailto:qli...@uc...>> wrote:
>>> Dear MUMmer develop team,
>>> 
>>> I am trying to use NUCmer together with mummer plot to compare different assemblies of the same plant genome (~640Mb) and my command is:
>>> nucmer --maxmatch -l 100 -c 100 -p compare1_2 assembly1.fasta assembly2.fasta
>>> mummerplot --png -p compare1_2 compare1_2.delta -R assembly1.fasta -Q assembly2.fasta
>>> 
>>> Both assemblies have hundreds of contigs, and thus the figure looks messy. Could you provide some instructions on tuning the parameters to better generate dot plot for two draft assemblies on contig level?
>>> 
>>> Thank you so much
>>> Qihua
>>> 
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>> 
>> 
> 
>