I am running mummerplot using the alignments of contigs against a reference genome.
My command to run mummerplot is this one:
mummerplot -p contigsvsreferencegenome -r Chr1 -t png --filter --layout Nucmer_c156_g1000_l1000_i90.mdelta
I would like to include in the plot only the contigs that align against chr1, so I tried the option -Q with a file with the names of the contigs, however, it is not working.
my file is something like
contig1 contig2 contig3
Do you know how I could remove the contigs without alignments from the plot?