I made taxonomic analys of 16S, and i got sequences with the following information:
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g__; s__
k__Bacteria; p__Bacteroidetes; c__Bacteroidia; o__Bacteroidales; f__; g__; s__
k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria
I almost forget, i used silva (13_8 & 13_5) and green genes (the most recient) databases in order to check differences, but i got similar assignments, then i made a manual blast of sequences getting more deep info or even another information (like the image below)
So my doubt is:
It is possible to make a reassignment (of thoose features/sequences) within qiime2 using command lines, metadata, etc? in case that dont, wich tools do you recommend for it?
because i need to have them well assigned (at least, at genus level) for another analysis
thanks for your time
I think you meant to say that you used GreenGenes (13_8 & 13_5) and version 138.1 of SILVA.
Can you provide more details about the sequences you are trying to classify? Are they full length sequences? A specific amplicon region, i.e. V4, V1V3, ...? What approach are you using to classify your sequences, classify-sklearn?
You can always use RESCRIPt to construct and optimize your own SILVA classifier.
How are you selecting your manual BLAST results? Taking the top hit? If so, be wary of that approach as quite often the top set of hits are equivalent and they are not necessarily sorted in any particular order. For example, your top ten hits can be exact matches to several different species or genera. In some cases the top few hundred hits are equivalent, and any hits to different taxa would go undetected unless you manually scroll through a few pages of top hits. This is quite common with short amplicon sequences, and precisely why the consensus-blast, and consensus-vsearch methods are provided.
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