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  1. IGB
  2. IGBF-3365

Prepping data and entries for SRA for Ravi / Kelsey data

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None
        • Story Points:
          3
        • Epic Link:
        • 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.

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              Task - A task that needs to be done. IGBF-3498 Review SRA Submissions

              • Major - Major loss of function.
              • Closed

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                26 older comments
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                robofjoy Robert Reid added a comment -

                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.

                Show
                robofjoy Robert Reid added a comment - 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.
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                robofjoy Robert Reid added a comment -

                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

                1. https://docs.google.com/spreadsheets/d/1Vy2M7cW8ZE7u3R6y5080kF_U1LwTgt-H/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
                2. https://docs.google.com/spreadsheets/d/14ZQt_FV2Eb66Ts8Yppbg_LKC3tQkROtO/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
                3. https://docs.google.com/spreadsheets/d/1at78HnfhJepNWiSON5lRrxbRhjI7njSW/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true

                Meta Tables

                1. https://docs.google.com/spreadsheets/d/1t6P-mfkKjG0B9ywqGbaOXC5NqjUSfvnt/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
                2. https://docs.google.com/spreadsheets/d/1d9rNnqbAMIF7RU_AdgvPsGVjLAw7yfBo/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
                3. https://docs.google.com/spreadsheets/d/1AeWPrDwqtGVYjYIdOqXYRKZpf1C-fHrO/edit?usp=drive_link&ouid=100714234126361751017&rtpof=true&sd=true
                Show
                robofjoy Robert Reid added a comment - 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
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                Mdavis4290 Molly Davis added a comment - - edited

                Review:

                Biosamples

                1. Good
                2. Good
                3. Good

                Meta Tables

                1. Good
                2. Good
                3. Good

                Note: I saw no issues with the data. Moving to Ready for PR which equals submitting the data if ready to NCBI.

                Show
                Mdavis4290 Molly Davis added a comment - - edited 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.
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                robofjoy Robert Reid added a comment -

                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.

                Show
                robofjoy Robert Reid added a comment - 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.
                Hide
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                robofjoy Robert Reid added a comment -

                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

                Show
                robofjoy Robert Reid added a comment - 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

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
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                      Updated:
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