getting NCBI ID problem

Hi, I have completed microbiome analyses of my samples. I will use the abundance of the microorganisms to train my project. However I have to use microorganisms' NCBI IDs instead of their names in my project. Is there a way to get the IDs? In movingpictures tutorial it says the rep-seq visualization provide NCBI blast links but it doesnt working. Is there another way?

Hi @kubra,
I am not sure I understand. I will need more information in order to assist.

Am I understanding correctly that you want to use NCBI IDS for your features/ASVs/OTUS instead of the hash that is generated from dada2

Is the rep-seqs blast link not working or is it not generating what you need? If its not working can you upload a screenshot of how it is not working?

Additionally, can you give an example of what data you are working with(like a feature table) what it looks like now, and what you want it to look like?

Thank you for your support. When I complete Taxonomic Analyses step in Moving Pictures Tutorial I obtain microorganisms' names in taxonomy.gza or barplot csv files. But I need those microorganisms' NCBI IDs.

It is so labor intensive to search them one by one. I wonder if there is an applicable method to do that

Hi @kubra,
Is classify-consensus-blast possible what you are looking for? Look into the docs and let me know: classify-consensus-blast: BLAST+ consensus taxonomy classifier — QIIME 2 2023.9.1 documentation

1 Like

Thank you @cherman2 I will try this option. I hope it works, thank you for your support🌸

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.