Closed mlvermeire closed 3 years ago
Hi Marie-Liesse,
I suspect the relevant information is in the description of the assignTaxonomy
training fasta format here: https://benjjneb.github.io/dada2/training.html#formatting-custom-databases
For IdTaxa
, I have not myself tried to create a custome reference for that function. IdTaxa
is defined in the DECIPHER R package, which has documentation here: https://bioconductor.org/packages/release/bioc/html/DECIPHER.html
See the "Classify sequences" document linked there, specifically Section 3 on training the classifier. @digitalwright Is there any additional online documentation that might help here?
@benjjneb, The Classifying Sequences vignette is the correct place to start. @mlvermeire, Please send me an email if you need more help. Erik
Dear @benjjneb and @digitalwright , thank you very much for your answers! I'll have a look at the documentation you sent and will keep you posted. I wish you a very good week, kind regards
Dear benjjneb, Thank you very much for this great pipeline! We are currently developing the metabarcoding approach to characterize nematode communities in our soil samples. We would like to construct a database for soil nematodes to use in the pipeline. I would like to ask you some questions concerning the steps to create a database in the appropriate format. We have a list of sequences, and the corresponding taxonomy. How do we need to format this data to be used in the idtaxa or assignTaxonomy function? Thank you very much in advance for your time and consideration. I wish you a very good day, Kind regards,
Marie-Liesse