Hi,

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?