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:3
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Epic Link:
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Sprint:Summer 3 2023 June 12, Summer 6 2023 July 24, Summer 7 2023 Aug 7, Summer 8 2023 Aug 21, Fall 6, Fall 7, Spring 1, Spring 2
Description
Prepare the sequence data from the 3 separate sequencing runs.
Rename the sequencing files to match the single letter coding format like we use in the Muday time course.
Create a Biosample Spreadsheet.
Create an SRA spread sheet.
Figure out what aspects of this project that require different entries compared to the Muday and Johnson projects.
Attachments
Issue Links
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- Closed
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Activity
I'll need to once over this.
The data is in the FTP location.
I will likely click send to NCBI.
And then post the IDs we get.
Review:
Biosamples
- Good
- Good
- Good
Meta Tables
- Good
- Good
- Good
Note: I saw no issues with the data. Moving to Ready for PR which equals submitting the data if ready to NCBI.
Review time !!
I would like a person to review 6 sheets below.
We have reviewed these before so things should be logical and correct.
Just look for logical errors.
Biosamples
- https://docs.google.com/spreadsheets/d/1Vy2M7cW8ZE7u3R6y5080kF_U1LwTgt-H/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
- https://docs.google.com/spreadsheets/d/14ZQt_FV2Eb66Ts8Yppbg_LKC3tQkROtO/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
- https://docs.google.com/spreadsheets/d/1at78HnfhJepNWiSON5lRrxbRhjI7njSW/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
Meta Tables
- https://docs.google.com/spreadsheets/d/1t6P-mfkKjG0B9ywqGbaOXC5NqjUSfvnt/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
- https://docs.google.com/spreadsheets/d/1d9rNnqbAMIF7RU_AdgvPsGVjLAw7yfBo/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
- https://docs.google.com/spreadsheets/d/1AeWPrDwqtGVYjYIdOqXYRKZpf1C-fHrO/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
NCBI SRA FTP location for SRA upload:
Establish an FTP connection using the credentials below:
Address: ftp-private.ncbi.nlm.nih.gov
Username: subftp
Password: HiomCukJophtEet3
The above credentials are temporary.
Starting the upload now.
the SRA and Biosample sheets will reside in Google drive:
https://drive.google.com/drive/folders/10-gf6u7fyzZijqvSN7vOzN5X-TmxEUa_?usp=drive_link
The plan is for all of the samples run in Ravi's lab to be submitted at once. The sequences were run in 3 separate sequencing projects via Azenta. The first was a pilot test run.
This is an automatic acknowledgment that your recent submission to the SRA database has been successfully processed and will be released on the date specified.
Please reference PRJNA1071054 in your publication. This BioProject accession number is provided instead of SRP and should be used in your publication as it will allow better searching in Entrez.
Accession to cite for these SRA data: PRJNA1071054
Temporary Submission ID: SUB14180617
Release date: 2024-01-30