I am analysing a study (with 96 samples, demultiplexed and paired-end). Some of the samples are bacterial (primers: 520f-802r) and others are fungal (primers: ITS1-ITS2)
I am on the taxonomic classification (using, qiime feature-classifier) step where I want to compare my data with some reference database. The SILVA database does not contain any database for both Bacteria and fungi. How should move ahead? Can you suggest me some other reference database? OR how can I separate my samples to analyse them separately?
Hi @SAHIL_JAIN_16110144,
Are these samples all from the same study/same run? Assuming the answer to both is yes then you really want to separate these samples right from the beginning after demultiplexing. Once they are separated you just go through the samples as you normally would with bacteria (using greengenes or SILVA as a reference database for example) and fungi (ITS, with UNITE database) separately. These databases can be found on their respected websites and also on the qiime2 data resource page.
A quick way to separate - assuming they are mixed together in the fastq file - could be to use cutadapt for each primer set seperately with a low error rate, and only keep sequences that have the primers trimmed.