Hello everyone,
Any public databases where I can share my 16S RNA data when I finish a microbiome study?
Thanks for any help!
1 Like
Hi @Rebeca_Mendez,
I think the official answers are ENA and SRA. I prefer ENA because it gets mirrored into SRA. (Anything I put in ENA shows up in SRA, the reverse is not true). Unfortunately, I dont have a great tutorial for submitting to either. I recommend budgeting like a working day to do the submission. Ive done a few, and its not so much hard as finicky.
I think if you have personal data the needs to be protected, dbGAP might be an option, but you'd need to check their documentation.
In all three cases, you probably want to follow the MixS metadata standards to figure out what minimum information to put in. ... IIRC, @cherman2 has a video on the QIIME 2 youtube on interoperable metadata.
IIRC, Qiita will also host your data, and can help you with ENA submission. However, I think Qiita only submits forward reads so if you used both in your analysis, this may or may not work for you. Qiita has some metadata guidance, which can be useful.
In addition to submitting to a formal repository, I also recommend looking putting together a GitHub repo for your analysis. I often put my working data there, including my metadata, a data dictionary for the metadata, my denoised feature table, and anything that took more than 3 hours to compute. A zenodo DOI can be a good way to help version that. I like having the parallel GitHub because there's a little more space for me to play.
I can share an example of how I integrated it in a recent manuscript, fi that would be helpful. But I'll also note there seem to be as many ways to submit data as there are people doing the analysis.
Best,
Justine
5 Likes
Justine thank you so much for such valuable information!
I will be looking into this sites and see if it works for me.
Thank you deeply for your insights. You´re the best!
R.
2 Likes