hi,I have a question about taxa database ,I’m a clinical bioengineer who detection the pathogenic bacteria .So ,the classifier about the sample is very importance , I want to set up a database about some Recurrent disease and some common pathogenic bacteria , I want to know this project whether or not come true . my plan is that we use the common pathogenic bacteria whole genome and the silva database to do intersection ,the last get a new database .but I don’t know the plan whether or not can achieve my aim .and I hope you can give me some advice to get the result .thank you !
Can you please clarify? It sounds like you want to classify sequences by comparing to a reference database of sequences from known pathogens. Is that correct?
Are you using marker gene amplicon sequencing? (e.g., 16S rRNA gene sequencing)
If so, you will want to extract the appropriate marker genes from your pathogen reference sequences. Comparing to SILVA will be a time-consuming and possibly fruitless process. Instead, you can use extract-reads or a similar method outside of QIIME2 to extract these marker genes from whole genome sequences of these pathogens. Then merge those sequences with SILVA sequences that have been trimmed to the same region. That becomes your reference sequences (and remember to also add the taxonomic lineages for each sequence to your reference taxonomy).
If your aim is to add certain pathogenic strains to the SILVA database, then yes that will achieve your aim.
I hope that helps.
yes, thank you give me the advice ,I think it very useful .but recently I meet a question ,when I classifier the sequence just have the class result ,I use the greengene database ,I use the database do other samples taxonomy is ok ,some project I can't success ,the result like this
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