Requesting complete information regarding localize functionality #571
Description
Hi @ArtRand ,
Thank you for all your efforts in developing modkit and answering queries!
Currently the information provided in the documentation regarding localize only appears in the Extended subcommand help.
It is not clear what functionality is provided by localize and how best to use it.
There is some relevant discussion at the end of #399 and it would be great to fully document this.
For my experiments in studying RNA modifications, after running dmr --segment I have a bed file of regions.
And after filtering the segment bed file for "different" categorized regions, and passing this to localize --chart with a window of just 10 nt, I assumed this would visualize modification patterns at the specific regions and stack the samples/replicates.
I passed top 10 differential regions based on a heuristic, and was expecting 10 plots, but I only obtained 1 plot per modification type per replicate.
Sorry, I do not understand how localize is working and how the regions are being considered/analyzed.
The initial expectation while using localize was to generate a plot like Fig. 3A which uses modPhred.
Since modPhred is obsolete, I thought localize is ONT's approach to visualize modifications in regions of interest.
Would be very helpful to have greater clarity about this.