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  1. IGB
  2. IGBF-3165

Make junction files for experimental and positive control alignments data

        Details

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

          Description

          Run the "find junctions" program to generate spreadsheets showing support for splicing events.

          This program generates bed format files that tabulate evidence supporting splicing. The "score" field of the output file indicates the number sequence alignments that exhibit evidence of splicing in a particular location, called a "junction".

          This format for representing splicing events comes originally from the "tophat" program, which generates "bed" files containing junctions in essentially the same way.

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              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-3172 Tabulate splicing support by running arabitag algorithm on junction and bam files

              • Major - Major loss of function.
              • Closed
              is blocked by

              Task - A task that needs to be done. IGBF-3143 Run RNA-Seq data processing pipeline on positive splicing control and experimental samples

              • 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 is blocked by IGBF-3143 [ IGBF-3143 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Summary Generate junction files for experimental and positive control alignments data Make junction files for experimental and positive control alignments data
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 1 2022 Aug 15 [ 153 ] Fall 1 2022 Aug 15, Fall 2 2022 Sep 5 [ 153, 154 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Link This issue blocks IGBF-3172 [ IGBF-3172 ]
                ann.loraine Ann Loraine made changes -
                Description Run the "find junctions" program to generate spreadsheets showing support for splicing events. Run the "find junctions" program to generate spreadsheets showing support for splicing events.

                This program generates bed format files that tabulate evidence supporting splicing. The "score" field of the output file indicates the number sequence alignments that exhibit evidence of splicing in a particular location, called a "junction".
                ann.loraine Ann Loraine made changes -
                Description Run the "find junctions" program to generate spreadsheets showing support for splicing events.

                This program generates bed format files that tabulate evidence supporting splicing. The "score" field of the output file indicates the number sequence alignments that exhibit evidence of splicing in a particular location, called a "junction".
                		Run the "find junctions" program to generate spreadsheets showing support for splicing events.

                This program generates bed format files that tabulate evidence supporting splicing. The "score" field of the output file indicates the number sequence alignments that exhibit evidence of splicing in a particular location, called a "junction".

                This format for representing splicing events comes originally from the "tophat" program, which generates "bed" files containing junctions in essentially the same way.
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
                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 ] 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 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]

                  People

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

                    • Created:
                      Updated:
                      Resolved: