I am analyzing some ITS-2 sequencing data using qiime2-2018.2 and had a few basic questions about methods I can use as alternatives to the OTU-picking pipelines. Specifically, is there currently an ITS-2 equivalent to the Deblur “qiime deblur denoise-16S” function? And is DADA2 set up yet to handle joined reads? Thanks in advance for your help!
As long as the data is Illumina sequences you can use qiime deblur denoise-other to denoise your ITS-2 data, though you do need to provide your own reference database such as one from UNITE or something else.
As DADA2 has it own merging protocols it requires the input to be unjoined raw sequence, in fact for optimal results they should not be filtered or quality controlled prior either.
Let us know if you have any more questions!
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