Entering edit mode
10 weeks ago
Art_SG ▴ 10
How to source taxonomy analysis accurately? The results in web browser are different than in
tax_analysis table in cloud.
Taking as an example
In web browser analysis is there
But when querying with AWS Athena:
SELECT * FROM "sra"."tax_analysis" WHERE acc = 'ERR1725012'
I have only single row of result:
Apparently it is ok for some accessions, but not for all. Am I doing something wrong? How to fetch the same taxonomy analysis that is available in a browser?
In that case, your best bet is to contact NCBI help desk with examples of what works and what does not. Post their response here once you get it.
Yes, I sent them a ticket about it already. I will post if have any reasonable response. So far for 70% datasets that I was trying result is as above - single row only with high level rank (but OK through web browser). Weird.
There have always been differences in web based results from NCBI and what you may get from command line tools. In this case if the data comes from the same location perhaps they are not making all of it available via that query.