Question: mummerplot for genome self alignment NOT yielding full length diagonal graph
0
gravatar for Anand Rao
23 months ago by
Anand Rao330
United States
Anand Rao330 wrote:

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!

Ath-ORIG-self-lc100-delta-1 Ath-ORIG-self-lc100-delta-g Ath-ORIG-self-lc100-delta-m Ath-ORIG-self-delta-m Ath-ORIG-self-delta-1 Ath-ORIG-self-delta-g

ADD COMMENTlink modified 22 months ago • written 23 months ago by Anand Rao330
3
gravatar for Anand Rao
22 months ago by
Anand Rao330
United States
Anand Rao330 wrote:

![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 Cpap-self-ref-mummerplot4

ADD COMMENTlink modified 22 months ago • written 22 months ago by Anand Rao330

Hi, what is the blue and purple color ?

ADD REPLYlink written 17 months ago by Picasa570
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