Upload Data To Sra Without Taxonomy Id

Question

[GAO Yang]

Hi there~

I want to upload some transcriptome raw reads that I sequenced, to the SRA database.

But one of the samples (sample J ) was a artificial hybrid progeny of two other species, and even not officially defined as a new specie yet. So , sample J won't have the Taxon ID which is necessary for the submission.

What should i do? Should I use the Taxon ID of one of the parental species (father/mother)? Or should I apply for a new taxon ID even it has not been accepted as a new specie?

Any suggestion, discussion or information will be greatly appreciated!

Thank you!

[Sean Davis]

I'd suggest contacting SRA directly. This is an important question and impacts the utility of the SRA database.

[Istvan Albert]

To expand on Sean's adice - if you do get the information from SRA please consider following up here and adding it as an answer.

Answer 1

[GAO Yang]

Yeah, I wrote 2 letters, one for NCBI, the other one directly to SRA. And both were replied soon :) The letter from NCBI services suggested me to apply for new taxon ID, and I should contact SRA for sure.

The letter from SRA said I could just used the taxon ID of either of parental species, and then explained in the sample description. Simple!

Now I am going to upload the data files, as soon as got the password for the SRA ftp server.

[Istvan Albert]

interesting, thanks for following up

[Sean Davis]

This approach seems less than optimal. SRA metadata should be computable, so suggesting to include what is essentially known contamination in a "note" seems counter to that. This is a problem for SRA, but I just wanted to point out that this an obvious problem with the suggested solution.