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  1. IGB
  2. IGBF-3246

Generate list of EBSeq-HMM clusters for varieties and conditions

        Details

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

          Description

          Run EBSeq-HMM on SL5 gene count files and report the lists of genes within each cluster.

          • Create a new git repository for clustering code within hotpollen for the code
          • Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system
          • Run EB-Seq on the merged file
          • Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
          • Share with collaborators: results files and markdown report

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3242 Run nextflow for seedlingPollen dataset

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3244 Run rnaseq pipeline on mark-2022-timeseries

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-2993 [ 21429 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3242 [ IGBF-3242 ]
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3244 [ IGBF-3244 ]
                Mdavis4290 Molly Davis made changes -
                Description Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

                * Create a new git repository for clustering code within hotpollen for the code
                * Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system
                * Run EB-Seq on the merged file
                * Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
                * Share with collaborators: results files and markdown report
                		Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

                * Create a new git repository for clustering code within hotpollen for the code
                *{color:#14892c} Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system {color}
                * {color:#14892c}Run EB-Seq on the merged file{color}
                * Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
                * Share with collaborators: results files and markdown report
                Mdavis4290 Molly Davis made changes -
                Description Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

                * Create a new git repository for clustering code within hotpollen for the code
                *{color:#14892c} Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system {color}
                * {color:#14892c}Run EB-Seq on the merged file{color}
                * Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
                * Share with collaborators: results files and markdown report
                		Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

                * Create a new git repository for clustering code within hotpollen for the code
                * {color:#14892c} Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system {color}
                * {color:#14892c}Run EB-Seq on the merged file{color}
                * Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
                * Share with collaborators: results files and markdown report
                Mdavis4290 Molly Davis made changes -
                Attachment mark-timeseries-SL5-salmoncounts.txt [ 17669 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Attachment EBSeq_tomato.Rmd [ 17670 ]
                Mdavis4290 Molly Davis made changes -
                Attachment all_data_clusters.csv [ 17671 ]
                Mdavis4290 Molly Davis made changes -
                Description Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

                * Create a new git repository for clustering code within hotpollen for the code
                * {color:#14892c} Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system {color}
                * {color:#14892c}Run EB-Seq on the merged file{color}
                * Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
                * Share with collaborators: results files and markdown report
                		Run EBSeq-HMM on SL5 gene count files *and* report the lists of genes within each cluster.

                * Create a new git repository for clustering code within hotpollen for the code
                * Create a new merged table with results from "seedlingPollen" and "mark-2022-timeseries" in the Charlotte cluster file system
                * Run EB-Seq on the merged file
                * Produce human-readable, usable text files with results and tracking information indicating the source of the data used and also the version of the code that was used
                * Share with collaborators: results files and markdown report
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                Mdavis4290 Molly Davis made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Assignee Molly Davis [ molly ]
                Mdavis4290 Molly Davis made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                Mdavis4290 Molly Davis made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                Mdavis4290 Molly Davis made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                Mdavis4290 Molly Davis made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                Mdavis4290 Molly Davis made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                Mdavis4290 Molly Davis made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                Mdavis4290 Molly Davis made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                Mdavis4290 Molly Davis made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    Mdavis4290 Molly Davis
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    2 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: