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  1. IGB
  2. IGBF-3881

Add samtools filter by and color by options for CR and CB tags

        Details

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

          Description

          For this ticket, explore the prospect of adding samtools tags to right-click filter function so that user can filter reads from the track based on samtools tags. For the purposes of this ticket, adding CR, cellular barcode sequence bases, as a filter option so that users can filter reads based on cell identifiers.

          Adding this filter may help in understanding the UMI count matrix and to make a plan to add features for single cell data.

            Attachments

              Issue Links

              is blocked by

              Task - A task that needs to be done. IGBF-3867 Create a release branch without Ensembl code in it

              • Major - Major loss of function.
              • Closed
              relates to

              Task - A task that needs to be done. IGBF-3897 Investigate Illumina sc-RNA-Seq

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-3907 Investigate adding additional Samtools tags to Filter/Color By options in IGB

              • Major - Major loss of function.
              • To-Do

              Task - A task that needs to be done. IGBF-3880 Investigate samtools tags consistency across datasets from Cell Ranger

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                karthik Karthik Raveendran created issue -
                karthik Karthik Raveendran made changes -
                Field Original Value New Value
                Epic Link IGBF-3765 [ 22984 ]
                karthik Karthik Raveendran made changes -
                Link This issue relates to IGBF-3880 [ IGBF-3880 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Assignee Ann Loraine [ aloraine ] Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Summary Investigate samtools tags filter Investigate samtools tags filter by and color by options
                karthik Karthik Raveendran made changes -
                Attachment After Filter by CR.png [ 18495 ]
                Attachment Before Filter by CR.png [ 18496 ]
                karthik Karthik Raveendran made changes -
                Attachment After Color by CR.png [ 18497 ]
                Attachment Before Color by CR.png [ 18498 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                karthik Karthik Raveendran made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Link This issue relates to IGBF-3899 [ IGBF-3899 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                karthik Karthik Raveendran made changes -
                Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ]
                pkulzer Paige Kulzer made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                pkulzer Paige Kulzer made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                pkulzer Paige Kulzer made changes -
                Assignee Paige Kulzer [ pkulzer ] Karthik Raveendran [ karthik ]
                karthik Karthik Raveendran made changes -
                Link This issue relates to IGBF-3897 [ IGBF-3897 ]
                nfreese Nowlan Freese made changes -
                Summary Investigate samtools tags filter by and color by options Add samtools filter by and color by options for CR and CB tags
                ann.loraine Ann Loraine made changes -
                Sprint Fall 1 [ 202 ] Fall 1, Fall 2 [ 202, 203 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                nfreese Nowlan Freese made changes -
                Link This issue relates to IGBF-3907 [ IGBF-3907 ]
                karthik Karthik Raveendran made changes -
                Link This issue is blocked by IGBF-3867 [ IGBF-3867 ]
                ann.loraine Ann Loraine made changes -
                Sprint Fall 1, Fall 2 [ 202, 203 ] Fall 1, Fall 2, Fall 3 [ 202, 203, 204 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                karthik Karthik Raveendran made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                karthik Karthik Raveendran made changes -
                Assignee Karthik Raveendran [ karthik ] Ann Loraine [ aloraine ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                nfreese Nowlan Freese made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                nfreese Nowlan Freese made changes -
                Assignee Ann Loraine [ aloraine ]
                nfreese Nowlan Freese made changes -
                Assignee Karthik Raveendran [ karthik ]
                nfreese Nowlan Freese made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                nfreese Nowlan Freese made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    karthik Karthik Raveendran
                    Reporter:
                    karthik Karthik Raveendran
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: