I used mummerplot to generate a dot plot. It looks pretty good except that there're 3 places that have double lines which seem due to issues of chromosome sorting and can be resolved if the order of the chromosomes are shifted, such as chromosome 4 and 7. Any idea what might have caused this and how to fix it? Thank you!
I ran the mummerplot using delta file from filtered nucmer output
I used mummerplot to generate a dot plot. It looks pretty good except that there're 3 places that have double lines which seem due to issues of chromosome sorting and can be resolved if the order of the chromosomes are shifted, such as chromosome 4 and 7. Any idea what might have caused this and how to fix it? Thank you!
I ran the mummerplot using delta file from filtered nucmer output
mummerplot -p test -t png -f -l -R ref.fa -Q query.fa nucmer_filtered