Documentation for files and their columns in results and other directories

[alexvasilikop]

Hello,

Thanks again for developing some useful tools. Is it possible that you can add some documentation-description of the output files in the results directory? Or is there somewhere where I can find this info?

In particular I am referring to the following files and their columns: syntenicBlock_coordinates.csv syntenicRegion_coordinates.csv Orthogroups.tsv N0.tsv combBed.txt

Same thing applies for the pangenome, syntenic hits directories.

Also I have some difficulty interpreting the legend for the dotplots (see below). what does score > 50, 11/11−gene x/y windows (heatmap range: 2−5+ hits/window) mean? Thanks Alex

[jtlovell]

Yeah, the documentation needs to be better and will eventually get there in the help file; however, the descriptions are in the various sub-functions and fully described in the tutorial tho.

[jtlovell]

I guess I need to improve the documentation for the heatmaps. This means blue is representing 1 hit per 11-gene intervals. Yellow is 5 hits or more.

[alexvasilikop]

Thanks, the score is referring to bitscore here?

[jtlovell]

diamond bitscore, yes.