I recently used ragtag to correct de novo assembled contigs and order and orient them to the pig reference genome using ragtag scaffold. I'd like to generate dotplots to assess the assembly. I've read a couple posts where people have suggested using mummerplot to do this; however, I cannot figure out how to use the output files from the ragtag scaffold command to generate these plots using mummerplot. I've tried using the query_against_ref.paf and ragtag.scaffolds.agp files as input for mummerplot, which produced the following error:
ERROR: Could not read ragtag.scaffolds.agp, Unrecognized file type
I also tried to use these files as input for show-tiling, which produced the following error:
ERROR: Could not parse delta file, ragtag.scaffolds.stats error no: 400
Does anyone have any advice on how to use ragtag scaffold output files to generate dotplots using mummerplot?