Hello everyone !
This is my first try using MUMmer, I would like to visualize something close to this publication : http://biorxiv.org/content/biorxiv/early/2016/12/02/090969.full.pdf (page 18). I'm trying to align the 6 longest contigs of my assembly to see where it aligns on D.melanogaster genome.
I've already tried something like that using mummer :
#Launching mummer ./mummer -b melanogaster.fasta suzukii_6first_contigs.fasta > mummer_mel_against_top6_canu.mums #Plot using mummer plot ./mummerplot -x "[0,250000]" -y "[0,250000]" -postscript -p mummer_mel_against_top6_canu mummer_mel_against_top6_canu.mums'
Each time I've tried something, the -x and -y options where required, but I don't know at which contigs from my assembly or which chromosomes to the ref it correspond too...
I've followed the example proposed here : http://mummer.sourceforge.net/examples/#nucmernucmer , but I can't find an example of how to create the same kind of plot I saw in the bioarXiv paper.
Anyone with some experience with mummer can help me understanding how the plots are working ?