mummerplot for genome self alignment NOT yielding full length diagonal graph

Question

[Anand Rao]

I am trying to obtain the classical diagonal plot for genome self alignment

For this, I am trying out my MUMMER syntax with a slightly processed Arabidopsis thaliana genome that can be downloaded from https://ufile.io/93muh

Syntax records are as shown below

STEP 1 - nucmer (2 variations in syntax, using -l -c or not)

nucmer --mum -l 100 -c 100 -p Ath_ORIG_self_lc100 Ath_ORIG.fasta Ath_ORIG.fasta
nucmer --mum -p Ath_ORIG_self Ath_ORIG.fasta Ath_ORIG.fasta

STEP 2 - delta-filter (2 *3 = 6 variations in syntax, delta-filter type -1, -m, or -g)

delta-filter -1 Ath_ORIG_self.delta > Ath_ORIG_self.delta.1
delta-filter -m Ath_ORIG_self.delta > Ath_ORIG_self.delta.m
delta-filter -g Ath_ORIG_self.delta > Ath_ORIG_self.delta.g
delta-filter -1 Ath_ORIG_self_lc100.delta > Ath_ORIG_self_lc100.delta.1
delta-filter -m Ath_ORIG_self_lc100.delta > Ath_ORIG_self_lc100.delta.m
delta-filter -g Ath_ORIG_self_lc100.delta > Ath_ORIG_self_lc100.delta.g

STEP 3 - mummerplot (6 mummerplots corresponding to 6 variant input files from the previous delta-filter step)

mummerplot Ath_ORIG_self.delta.1 --layout -R Ath_ORIG.fasta -Q Ath_ORIG.fasta --png -p Ath_ORIG_self.delta.1 -t Ath_ORIG_self.delta.1
mummerplot Ath_ORIG_self.delta.m --layout -R Ath_ORIG.fasta -Q Ath_ORIG.fasta --png -p Ath_ORIG_self.delta.m -t Ath_ORIG_self.delta.m
mummerplot Ath_ORIG_self.delta.g --layout -R Ath_ORIG.fasta -Q Ath_ORIG.fasta --png -p Ath_ORIG_self.delta.g -t Ath_ORIG_self.delta.g
mummerplot Ath_ORIG_self_lc100.delta.1 --layout -R Ath_ORIG.fasta -Q Ath_ORIG.fasta --png -p Ath_ORIG_self_lc100.delta.1 -t Ath_ORIG_self_lc100.delta.1
mummerplot Ath_ORIG_self_lc100.delta.m --layout -R Ath_ORIG.fasta -Q Ath_ORIG.fasta --png -p Ath_ORIG_self_lc100.delta.m -t Ath_ORIG_self_lc100.delta.m
mummerplot Ath_ORIG_self_lc100.delta.g --layout -R Ath_ORIG.fasta -Q Ath_ORIG.fasta --png -p Ath_ORIG_self_lc100.delta.g -t Ath_ORIG_self_lc100.delta.g

As you can see from the linked images, only 2 of 5 large chromosomes are showing the expected diagonal, but not the other 3 large chromosomes. Why is that? And how should I modify my syntax or add / subtract steps to obtain the graph I am looking for? Thanks!

Answer 1

[Anand Rao]

![enter image description here][1]Solved it: it was the syntax that was wrong (for MUMMER version 4)

Plus. I've chosen to use mummer rather than nucmer for step 1, as follows:

mummer -mumreference $IN $IN -l $MIN_CONTIG_LEN -threads 12 > $MUMS

Followed by step 2: mummerplot

mummerplot $MUMS --png -t $GRAPH_OUT -p $GRAPH_OUT -Q $IN -R $IN

These lines gave the characteristic diagonal plot for genomes self alignment. Leaving this solution out because it took me some time to dig through several possible syntax options to arrive at these. And the future seeker may save himself / herself that time :)

One example linked here

[Picasa]

Hi, what is the blue and purple color ?