Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:2
-
Epic Link:
-
Sprint:Spring 5 2023 Mar 6, Spring 6 2023 Mar 20, Spring 7 2023 Apr 10, Spring 8 2023 Apr 24, Spring 9 2023 May 1, Summer 1 2023 May 15
Description
Goal:
To prepare the sequence and metadata needed for SRA submission.
This is for Mark Johnson's Mature Pollen and Seedling data.
Attachments
Issue Links
Activity
Dear Robert Reid,
This is an automatic acknowledgment that your submission:
SubmissionID: SUB13087168
BioProject ID: PRJNA975110
Title:
has been updated, eg by the linkage of one or more BioSamples. The locus_tag prefixes for
each linked BioSample are included in the locustagprefix.txt file that can accessed
from this BioProject in the submission portal:
https://submit.ncbi.nlm.nih.gov/subs/bioproject/SUB13087168/overview
In addition, you can view the locustagprefix.txt files for all of your BioProjects from the BioProject submission page,
https://submit.ncbi.nlm.nih.gov/subs/bioproject/.
Please use the BioProject ID PRJNA975110 with your correspondence and your data submissions.
Send questions to bioprojecthelp@ncbi.nlm.nih.gov, and include the BioProject ID and organism name.
I searched for "PRJNA975110" using the SRA interface but nothing was found.
attn: [~RobertReid]
We need to get a spreadsheet that maps our sample codes onto their corresponding SRR accessions.
It needs the following columns:
- SRR value
- Sample code
Let's keep track of this new work using this same ticket. Re-opening the ticket pending this final last bit of work!
I was able to log into the SRA and get a spreadsheet with sample submission information that maps SRR accessions onto our sample codes. Attaching it here.
For the next steps, we should create a new repository for this particular dataset.
Changed the release date to "immediately".
NCBI response:
Your data will be released after we process this date change from 2024-07-01 to 2023-05-30.
This may take a few hours but most requests will be processed sooner.
Rob has the raw sequences both on cluster and locally on a backup at the following location:
/Volumes/Promise Pegasus/oat/tomato/johnson-jan22/30-614759823/00_fastq
(This location is easiest for the FTP transfer to NCBI)
Total files = 96.
Total R1 files = 48
Total R2 files = 48
Md5sum results are here also and are needed for the FTP transfer.
Biosample TSV table: Can be found here in the GTTR group experiments folder:
https://docs.google.com/spreadsheets/d/1WDfAbXmA-sdGSx4TF1-56FtXNS_G0CeOFPz5xoRFGR0/edit?usp=sharing