Remove sequences without alignment in mummerplot

Question

[Corentin]

Hi,

I aligned a scaffold assembly to a closely related species with Mummer. So, this is a "many vs one" approach.

I am happy with the tool. However, when I produce the dot plot on the filtered alignments (I used delta-filter using the "-1" option to get unique alignments) the plot contains scaffolds without any alignments (cf upper part of the plot below).

I would like to remove them. I can manually remove them from the "out.gp" file but is there a way to do it directly with mummerplot ? I did not find anything in the user manual. Another solution would be to write a script that modify the "out.gp" file but how to find the sequence ids that have no alignments ?

[Sej Modha]

Did you try --filter in mummerplot?

[Corentin]

I tried but the sequences still appear in the dot plot, like before as an empty line.