Blast representative sequences against NCBI corresponding selected samples

[LuciaGG]

Hello everyone,

I have analyzed my 16S data and perfomed the taxonomic classification using qiime feature-classifier classify-sklearn \ with the greengenes database. Some samples
are assigned at the order or genus level, which is to be expected since the amplicons are 190 bp in lenght.

However, I would like to blast against NCBI the representative sequence of the mentioned samples. How can I select the representative sequence of each sample that I want to compare with blast?

Thanks in advance,

Lucia

[jwdebelius (Justine Debelius)]

Hi @LuciaGG,

You could try filtering the table or sequences to remove undefined taxa using the filter-seqs or filter-table in the q2-taxa plugin. I think if you tabulate the sequences (qiime feature-table tabulate-seqs), you can click on the sequence and that will blast them.

Best,
Justine