Is there a new reproducible example?

[kieft1bp]

I'm interested in using the program to visualize my data, but the example code provided here (https://thackl.github.io/gggenomes/articles/emales.html) is broken in several place. I can't reproduce any visualizations or data frames given the data files provided (e.g., emales.fna, etc.). I saw the disclaimer at the top, so I wasn't expecting any miracles - but, do you have a new, update set of commands that would actually generate the correct data tables for plotting?

[iimog]

The documentation has example code for most functions in the reference. E.g. for loading fasta and gff files there is https://thackl.github.io/gggenomes/reference/read_tracks.html Once you have your data loaded you can look at this example for inspiration. Also some advanced functions like flip and focus have detailed examples. I agree that a fully reproducible tutorial is desirable and I hope that we'll be able to re-add one. In the meantime, feel free to ask here if you get stuck with a specific problem.

[SLAment]

Terribly sorry if this is the wrong place to ask, but I'm also going through the old example, and now I'm stuck with this line: cluster-ids -t "cog%03d" < emales-mmseqs_cluster.tsv > emales-cogs.tsv What is this cluster-ids? Does it come from a specific program? I realize this is not exactly a gggenomes problem, but I would like to reproduce the example with my data :). Thanks, love the package so far!

[iimog]

The cluster-ids program is part of the thackl/seq-scripts by @thackl. You can find it in the bin directory.