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ravel-lab / VALENCIA

VAginaL community state typE Nearest CentroId clAssifier
MIT License
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Converting from Qiime2 #1

Closed akknight closed 4 years ago

akknight commented 4 years ago

Hi- I'm interested in using this tool, but my output data is from Qiime2 so there are several ASVs that would fall into each of the species/genus categories in the reference. Do you have any suggestions as to how the data could be reformatted into what gets input into the package?

michaelfrance commented 4 years ago

Hi, The general approach would be to sum read counts to ASVs belonging to the same taxon (e.g. all L. crispatus ASVs get summed). If you can provide me with an example of your file format I would be happy to write a script to achieve this.

michaelfrance commented 4 years ago

Hi, I have added a script which converts the output from Qiime2 to input for VALENCIA. Expected inputs are the ASV taxon name key file and the ASV counts table.