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  1. IGB
  2. IGBF-3190

Create sample sheet with categorical classifications per sample

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
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          Description

          We need a computer-readable document (e.g., ".csv" or ".xlsx Excel document) that records attributes of the "SRR" sample names:

          • SRP accession (SRA project)
          • SRR accession
          • Genotype
          • Plant Part (tissue type)
          • Treatment (type of control or temperature of treatment or ...)
          • Duration of treatment, e.g., time point
          • Some type of code to signal replicate samples, e.g., "a" for one group, "b" for another

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              Mdavis4290 Molly Davis added a comment - - edited

              Sample Sheet on google drive:
              https://docs.google.com/spreadsheets/d/1eXPF44kgVUMsqLr4wxZ33RpBIHXjXTbJwWXOUIPp8_Y/edit?usp=sharing

              Link to where data was collected to make sample sheet:

              SRP328042: https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=1&WebEnv=MCID_63443e01c38d1b07b351be48&o=acc_s%3Aa

              SRP252265: https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=2&WebEnv=MCID_63443e01c38d1b07b351be48&o=acc_s%3Aa

              Drought time (4 days) was determined by reading the research paper:
              https://www.mdpi.com/2073-4409/10/7/1809/htm

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              Mdavis4290 Molly Davis added a comment - - edited Sample Sheet on google drive: https://docs.google.com/spreadsheets/d/1eXPF44kgVUMsqLr4wxZ33RpBIHXjXTbJwWXOUIPp8_Y/edit?usp=sharing Link to where data was collected to make sample sheet: SRP328042: https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=1&WebEnv=MCID_63443e01c38d1b07b351be48&o=acc_s%3Aa SRP252265: https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=2&WebEnv=MCID_63443e01c38d1b07b351be48&o=acc_s%3Aa Drought time (4 days) was determined by reading the research paper: https://www.mdpi.com/2073-4409/10/7/1809/htm
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              Mdavis4290 Molly Davis added a comment - - edited

              Updated and uploaded sample sheet .csv and .xlsx file to cluster.

              Commands:
              rsync /Users/mollydavis333/Desktop/sample_sheet.csv mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/alt_splicing

              rsync /Users/mollydavis333/Desktop/sample_sheet.xlsx mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/alt_splicing

              Directory:
              /nobackup/tomato_genome/alt_splicing

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              Mdavis4290 Molly Davis added a comment - - edited Updated and uploaded sample sheet .csv and .xlsx file to cluster. Commands: rsync /Users/mollydavis333/Desktop/sample_sheet.csv mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/alt_splicing rsync /Users/mollydavis333/Desktop/sample_sheet.xlsx mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/alt_splicing Directory: /nobackup/tomato_genome/alt_splicing
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              ann.loraine Ann Loraine added a comment - - edited

              Added above Excel spreadsheet above to the repository.
              Moved to Done.

              Show
              ann.loraine Ann Loraine added a comment - - edited Added above Excel spreadsheet above to the repository. Moved to Done.

                People

                • Assignee:
                  Mdavis4290 Molly Davis
                  Reporter:
                  ann.loraine Ann Loraine
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                  • Created:
                    Updated:
                    Resolved: