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Old 04-12-2013, 06:00 AM   #1
struggler
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Location: UK

Join Date: May 2012
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Unhappy nucmer output plots

Dear All,
I have run nucmer and successfully generated *.coords, *.delta and delta-filter files. However, I am unable to generate dot plots or any other graphical output.

I am using the command:
mummerplot ref_qry.delta -R <ref.fasta> -Q <qry.fasta --filter --layout

Could anyone please help me to generate the suitable graphical outputs?

Regards,
S
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Old 04-12-2013, 06:22 AM   #2
GenoMax
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Do you have program "gnuplot" available on this machine? That is needed to generate the actual plots. http://mummer.sourceforge.net/manual/#mummerplot

If you are accessing the server from a PC/Mac using SSH and want to generate the plots then you will also need X11 (X-windows) program (and x-tunneling) to display the plots on local desktop.
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Old 04-12-2013, 06:33 AM   #3
struggler
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Thanks GenoMax!
Yes, I do have "gnuplot" up and running?

I am accessing the server from VMWare using SSH.

I don't know much about X11 (X-windows) program (and x-tunneling) but have generated graphical outputs from some other programmes.

I shall check this further.

Regards,
S
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