the difference between spliced pangenome graphs and pantranscriptomes

[jwli-code]

I don't understand the difference between spliced pangenome graphs and pantranscriptomes. Aren't the commands the same? https://github.com/vgteam/vg/wiki/Transcriptomic-analyses
I used MC's workflow to construct a graph genome, and then I found that the construction methods for Spliced pangenome graphs and Pantranscriptomes are exactly the same. I want to do the subsequent VPRG analysis. But I found that the command for Spliced pangenome graphs is

vg rna -p --threads <threads> --transcripts annotation.[gtf|gff3] --use-hap-ref --gbz-format graph.gbz > spliced_graph.pg
The command to construct transcriptomic analysis is
vg rna -p --threads <threads> --transcripts annotation.[gtf|gff3] --use-hap-ref --gbz-format --write-gbwt pantranscriptome.gbwt --write-info pantranscriptome.txt graph.gbz > spliced_graph.pg
It seems like the difference is only between these two parameters --write-gbwt pantranscriptome.gbwt --write-info pantranscriptome.txt , but these two parameters are just one output, which I don't quite understand. Maybe there is an issue with the input of the transcript file. I used the genome I constructed and provided all the GFF information for each genome.

[jwli-code]

@ekg @ktym @GaretJax @kevyin Hi，I would greatly appreciate it if you could take the time to address my issue.