Post date: Nov 03, 2014 8:51:38 PM
Here are the commands I used to summarize the L. warner (R) by L. sierra (Q) aligntment:
1. To generate information on the start and stop points of alignment and % similarity,
show-coords -rlc mumLsierra_Lwarner.delta > mumLsierra_Lwarner.coords
Note, % similarity was high overall, i.e. > 90% and often > 98%.
2. Filter to one-to-one alignment,
~/Source/MUMmer3.23/delta-filter -1 mumLsierra_Lwarner.delta > one2one_mumLsierra_Lwarner.delta
3. Make the dot plot (filter might be redundant with 2)
~/Source/MUMmer3.23/mummerplot one2one_mumLsierra_Lwarner.delta -R /labs/evolution/data/lycaeides/whole_genomes/Lwarner/DATA/RUN/ASSEMBLIES/assem12oct14/final.assembly.fasta -Q /labs/evolution/data/lycaeides/whole_genomes/Lsierra/DATA/RUN/ASSEMBLIES/assem15sept14/final.assembly.fasta --filter --layout -p plot_one2one_mumLsierra_Lwarner
The results look cleaner than before, but there still are short alignments/cluster. I am going to run this again with more stringent options to see what happens. Here is the command, which is the same as before but increases the minimum coverage size to 1000 bp,
/home/A01963476/Source/MUMmer3.23/nucmer --mum -c 1000 -l 15 -g 1000 --prefix=mumLsierra_Lwarner1k Lsierra/DATA/RUN/ASSEMBLIES/assem15sept14/final.assembly.fasta Lwarner/DATA/RUN/ASSEMBLIES/assem12oct14/final.assembly.fasta
I am also trying a melissa to melissa alignment with the same paramters.