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benjjneb / dada2

Accurate sample inference from amplicon data with single nucleotide resolution
http://benjjneb.github.io/dada2/
GNU Lesser General Public License v3.0
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Extraction of ITS region prior to taxonomic assignemnt #428

Closed gcuster1991 closed 6 years ago

gcuster1991 commented 6 years ago

Using DADA2 is it necessary to extract the ITS region using something like ITSx( http://microbiology.se/software/itsx/) prior to taxonomic assignment? If so how would one go about this?

nagasridhar commented 6 years ago

You can use the standard DADA2 workflow and at the taxonomic assignment step, you can point it to UNITE database. That will help you assign taxonomy to your dataset.

gcuster1991 commented 6 years ago

Hi @nagasridhar, Thank you for the response. I have used the UNITE database but I'm trying to understand how ITS sequence clustering and taxonomic assignment via DADA2 (without ITSx) compares to other methods that first extract the ITS region.

Is there something in the DADA2 pipeline that replaces this or does the same function?

thanks

benjjneb commented 6 years ago

@gcuster1991 I saw that you posted on another issue, did you get this issue resolved?

gcuster1991 commented 6 years ago

It appears others are using ITSx to safely remove sequences which haven't assigned to K__Fungi. I believe this answers my question. Thank you.