Describe provenance of Geoduck RNA-seq on NCBI SRA

[sr320]

Thinking about geoduck RNAseq (NS and Hiseq) provide a description of the relationship of
https://sr320.github.io/Illumina-Summary/

to what is on SRA - (Notebook post is fine and likely already exists :)

[kubu4]

Notebook entry is here:

https://robertslab.github.io/sams-notebook/2016/12/21/sample-submission-geoduck-tissue-gdna-for-illumina-pilot-sequencing-project.html

The TL;DR is that we sent tissue to Illumina and they did everything else. All tissue from single geoduck.

[sr320]

Thanks! I am looking for how to match these with SRAs

[kubu4]

I don't think I understand fully what you're looking for. The info is in nightingales spreadsheet.

[kubu4]

[kubu4]

The last column in the screencap above is the SRA BioProject accession.

[kubu4]

Sorry for being a dolt (still getting my head into "work mode"). I just realized what you're looking for! BRB...

[kubu4]

Do you want accessions which lead to this NCBI page (NCBI "Run"):

or do you want accessions which lead to this NCBI page (NCBI "Accession"):

[kubu4]

Or, this NCBI page (NCBI "Run Selector"):

[kubu4]

Now that I've posted all that above, I'll just put together a notebook which links to each one! How about that??!! :)

[kubu4]

New notebook entry is below. Let me know if you want me to make any changes.

https://robertslab.github.io/sams-notebook/2021/07/12/Summary-Geoduck-RNAseq-Data.html

[sr320]

So cross-referencing with https://sr320.github.io/Illumina-Summary/

looks like

NR-21-Larvae-d5
and
Geoduck-larvae-day5-RNA-EPI-99

are not in SRA?

[kubu4]

They are. I just neglected to incorporate them... Sorry!

[sr320]

Could you also go ahead and list seq platform in the table also?

…

On Mon, Jul 12, 2021 at 11:13 AM kubu4 ***@***.***> wrote: They are. I just neglected to incorporate them... Sorry! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1247 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABB4PNZNXUUGXORNRBUVZ53TXMWCFANCNFSM47SXO4ZQ> .

[kubu4]

Update has been pushed. Might take a few mins to update.