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  1. IGB
  2. IGBF-3042

Get RNA-Seq data from SRA

        Details

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

          Description

          Create and run a script (fasterq-dump-rnaseq.sh) that retrieves RNA-Seq data files from the SRA and converts them to fastq format.

          See linked issue for a comment containing a first draft of the script code: IGBF-3040

          Put script under version-control in:

          • salty_rice/bseq_rice/src

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3040 Create samplesheet with SRR run identifiers and experimental attributes

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-3039 [ 21553 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 2022 Jan 18 - Jan 28 [ 137 ] Spring 1 2022 Jan 3 - Jan 14 [ 136 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked lower
                ann.loraine Ann Loraine made changes -
                Description Create and run a script (fasterq-dump-rnaseq.sh) that retrieves RNA-Seq data files from the SRA and converts them to fastq format.

                Put script under version-control in:

                * salty_rice/bseq_rice/src                 		Create and run a script (fasterq-dump-rnaseq.sh) that retrieves RNA-Seq data files from the SRA and converts them to fastq format.

                See linked issue for a comment containing a first draft of the script code: IGBF-3040

                Put script under version-control in:

                * salty_rice/bseq_rice/src
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3040 [ IGBF-3040 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 1 2022 Jan 3 - Jan 14 [ 136 ] Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28 [ 136, 137 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Dates

                    • Created:
                      Updated:
                      Resolved: