Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:2
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Epic Link:
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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
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.
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 searched for "PRJNA975110" using the SRA interface but nothing was found.
attn: [~RobertReid]
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.
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
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.