Pulling sequences by blast in dada2

[Kakashi sensei]

Hello

I used Qiime to analyse previous sets of my data and it was pretty successfull.

For the sake of learning new tools, I recently started exploiting the dada2 R package to analyze a new set of data. Im trying to analyze 16s reads, assign taxonomy to them and then more importantly pull out a specific microbial species (subject of my research) and try to make inference on its diversity and abundance. 

assigning taxonomy to the whole microbiome wasn't hard. Challenge came when I tried to separate my target species. I already asked in the github forum and still seeking a reply but:

- would there be an equivalent of exclude_seqs_by_blast.py that I can use directly in dada2?

-if not, do I need to convert the sequence table from dada into a biom format table, import it into QIIME and simply run exclude seqs_by blast.py (maybe will also need to implement the mapping file in such case)  or do I need to repeat the whole analysis from scratch?

I would appreciate any help or advice on this matter.

Thanks a lot

[zhiying Guo]

Hello,

Sorry for the late answer. I followed the tutorial provided by dada2. But couldn't find an object (dataframe or list) which related reads label to consensus lineage. So I think target species sequence couldn't be directly generated from dada2

. 

Using exclude seqs_by blast.py is an alternative method.  Before using this qiime script, reference sequence could be obtained from assignTaxonomy result of dada2. By that way, biom convert is not needed.

QIIME2 has provided dada2 app, which is also an alternative method.

Hope it helps.

Zhiying Guo

[kyli...@gmail.com]

Hi,

Do you mean you want to pull the sequences of specific species and save them in a fasta files? 

Dada2 has a function uniquesToFasta() which allows you save the sequences in the OTU table as a fasta file. What I did is to find the sequences assigned to a specific species in the tax table and subset those sequences in the abundance table. Then I use the function to save those sequences in a fasta file.  

[zhiying Guo]

Hello, 

I did mean pull all the sequence (not in otu table or derep file) of specific species and save them in a fasta file. Usually I do this when re-analyze specific taxa.

if you just want pick all the sequence which existed in otu table, it is easy as out table is a "matrix". Besides, you can also pick them from  the "assignTaxonomy" result by writing it to csv file.

Zhiying Guo