Question about doall command

[Valentin-Bio]

Hello, I ran gapseq doall to determine the full metabolic network of my bacteria of interest. I ran it as the tutorial recommends:

gapseq doall assembly.fa

I was reading the stdout info that I saved into a .log file and I see that gapseq makes us of a medium 'assembly-medium.csv'. Is this medium a general medium for any taxon? or is this medium generated by gapseq medium command ?

Second, my purpose is to graph the metabolic reactions and enzymes that are involved in the production of X metabolite, How would you recommend me to do this from the gapseq output files ? shoudl I make use of the xml file to graph a specifific pathway in R?

best regards,

Valentín.

[Waschina]

Hi Valentín,

The medium is generated by the gapseq medium module.

Concerning your second question: There are a number of tools/packages for metabolic network visualisations. Most of them take SBML files as input. Thus, I recommend to use the xml-file output.

Best
Silvio