glennhickey
commented
1 year ago There's an XML file in Cactus where you can change this: https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/src/cactus/cactus_progressive_config.xml#L390-L392
Either directly in your installation, or make a copy of it, edit it, then pass the copy to any cactus command with the --configFile option.
You may still find it easier to play with odgi yourself. To do this, I'd recommend using the --chrom-og option. This will make a separate odgi graph for each chromosome (which is what --viz uses).
https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md#odgi
Hello,
I was hoping for help on two issues:
1) I'm currently running cactus-pangenome with the extra option --viz to produce a graph. I was wondering if it was possible to add extra options to my --viz command? For example, I wish to use odgi viz with -S, to show forward and reverse alignments within the graph.
2) Secondly, I produced a og file using --odgi. Afterwards, I tried to run odgi separately on the og file to produce a graph, however, the graph is not compact. There are many more path names in the graph, unlike when I run it through cactus-pangenome where it only has the names of the supplied input file. I checked the output for cactus-pangenome and I assumed the option -M was used to compact the graph. However, I tried with no success. I was wondering if there was an example, of how to use the -M option to compact the graph?
Thank you for any help you can provide!