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yphsieh / 16S-ITGDB

An integrated database for improving taxonomic classification of 16S Ribosomal RNA sequences.
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compatibility with R at the end of dada2 pipeline #2

Closed callmcgovern closed 1 year ago

callmcgovern commented 1 year ago

Hello, I just processed my 16s data with the dada2 pipeline and I am at the Assign Taxonomy step. I was trying to use the ITGDB database to assign taxonomy but I am getting errors that the file is not in the correct file format for the assignTaxonomy function. Do you know if I can make this work in R studio using this function? Thank you!

cil6758 commented 1 year ago

Hi, callmcgovern: Sorry for the late reply and thanks for raising this issue. 16S-ITGDB also supports DADA2 function in QIIME2 pipeline. So, 16S-ITGDB could also work with DADA2 package in R language, just like QIIME2.

Best regards

callmcgovern commented 1 year ago

Thank you @cil6758 . I figured it out and it worked :)