Group a set of plots using MUMmer

Question

[Rox]

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 ?

Cheers,

Roxane

Answer 1

[skbrimer]

It looks like it is actually 6 MUMer plots. The paper says they took their 6 largest contigs and mapped it against the 6 D.melanogaster chromosomal arms. I do not know anything about the fruit fly genome so I do not know if you need to make a multi-fasta of all the arms or not, but you would only map one contig to 6 arms. So to recreate the figure you would need to make that plot for each contig and then place neatly together after the fact.