Regarding Databases

can anyone guide me from where i can get pre-formatted databases for ready to run 18s rRNA data analysis ??

Hi @Jaykishan_Solanki, welcome to :qiime2:!

You can make use of the pre-formatted SILVA database, which includes all the SSU gene sequence data (i.e. 16S and 18S), from the Data resources page.

Alternatively, you can use the RESCRIPt plugin to curate the SILVA database as you'd like, as outlined here. You can also follow any of the other tutorials outlined on the GitHub page too.

1 Like

Thank you for the quick response. the data source page which you have pointed include Silva database for 16s as well as 18s so, are we supposed to separate them or we can use as it is. also do we need to import sequence and taxonomy file separately and generate classifier ?

but could you also guide me on which database to be used for denoising using Deblur

Hi @Jaykishan_Solanki,

There is no need to separate the 16S and 18S. They are homologous SSU (small subunit) rRNA gene sequences.

I'd recommend working through the tutorials, there are examples within these that highlight deblur, as well as this specific tutorial for using deblur on paired-end reads.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.