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metabaRfactory / metabaR

metabaR is an R package to curate and visualise DNA metabarcoding data after basic bioinformatics analyses.
http://metabaRfactory.github.io/metabaR
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Qiime2 to metabaR #41

Open martinjfsupagro opened 2 years ago

martinjfsupagro commented 2 years ago

Hello there, anyone already designed a script to import data from Qiime2 to metabaR? Would be very useful. Thanks !

lionncle commented 2 years ago

Hello,

Can you be more precise in your question? And detail your request because as it is, we cannot answer your request. It would be nice if you could describe the type of data to be imported.

For information, the data structure we use was mainly developed to be used with obitools. It will not be easy to convert data from other tools to be used with metabaR because a lot of information required for the package to work properly may be missing. If you think that Qiime2 can provide all this information and you detail the data generated by Qiime2 we may be able to make an import script. Otherwise it is impossible to modify our structure to use the data from Qiime2, it would harm the proper functioning of the package.

Thanks for your feedback

martinjfsupagro commented 2 years ago

The four tables that are required to build a metabarlist are quite standard indeed and are tweaks for the Qiime2 outputs. I was checking whether someone already made a full import script from the Qiime2 outputs as the community is huge and there are probably people who already did that but if nobody answer this in a couple of days I will post here (unless you have a forum that I could not find yet) an import script as it will be helpful to increase the use of metabaR and I need it anyway .