celine-mercier
commented
3 years ago Hi Irene,
You should be able to do it with obifiles_to_metabarlist (https://metabarfactory.github.io/metabaR/reference/obifiles_to_metabarlist.html) using those files:
file_obitab: path to the file produced by an export to tab format of the ecotag result (the command should look likeobi export --tab dms/ecotag_result > output.tab)file_ngsfilter: path to the ngsfilter file (the same file that you imported in the dms if you used ngsfilter)file_samples: path to a 'sample characteristics table'. This does not exist in the OBITools3, it should look like this file here, but I believe that it can simply be the list of sample names with one sample per line.
I'm supposed to make a function to import OBI3 data seamlessly but haven't done it yet..... might look into it these days if I can.
Please tell me if that works and ask for more information if needed :) Cheers Celine
IreneGregori
In order to create a metabarlist file, I must create 4 different files (motus, pcrs,..). How can I create those files starting from an Obitools3 output? In particullary, which files do I have to take from all the outputs made by Obitools3? Thank you