I am excited to use Mummer/Nucmer, and am running an alignment between a
couple of small datasets and comparing this to the output from a Mauve
alignment (same data).
My ref dataset has 3 contigs, my query dataset has 4. For some reason, a
large portion of one of the contigs in the query dataset appears to have
moved to a different contig. The query contigs (C4s12 and C4s13) are of
nearly the same length, but in the Nucmer alignment, C4s12 is much shorter,
and the missing region appears to be attributed to C4s13.
This obviously has huge ramifications on the interpretation of genome
reorganization events, which is what I am working on. Please see attached
image showing both Mauve and Nucmer alignments, with the region of interest
circled in red.
I am running Mummer 4.0, with the following commands:
Nucmer 1.c5.fasta 2.c4.fasta
show-coords -c out.delta > out.coords
And then viewing the results using an R script called DotPlotly.
mummerCoordsDotPlotly.R -i out.coords -o out -s -l -x -q 100000
Hello,
I am excited to use Mummer/Nucmer, and am running an alignment between a
couple of small datasets and comparing this to the output from a Mauve
alignment (same data).
My ref dataset has 3 contigs, my query dataset has 4. For some reason, a
large portion of one of the contigs in the query dataset appears to have
moved to a different contig. The query contigs (C4s12 and C4s13) are of
nearly the same length, but in the Nucmer alignment, C4s12 is much shorter,
and the missing region appears to be attributed to C4s13.
This obviously has huge ramifications on the interpretation of genome
reorganization events, which is what I am working on. Please see attached
image showing both Mauve and Nucmer alignments, with the region of interest
circled in red.
I am running Mummer 4.0, with the following commands:
Nucmer 1.c5.fasta 2.c4.fasta
show-coords -c out.delta > out.coords
And then viewing the results using an R script called DotPlotly.
mummerCoordsDotPlotly.R -i out.coords -o out -s -l -x -q 100000
Thank you for any advice,
Jon
I found that the issue is in the R script DotPlotly. This problem results when DotPlotly -m is set to 5kb or higher.