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  1. IGB
  2. IGBF-3897

Investigate Illumina sc-RNA-Seq

        Details

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

          Description

          Situation: Spoke with Matt Sergent (msergent@illumina.com) who is the local area rep for Charlotte. He said he is frequently on campus if we had questions. He mentioned that Illumina works differently in how they label each cell, and that they are not using UMI values. It's unclear if that means the BAM file will have the samtool tag for the cell barcode (CB/CR?).

          I also asked if Illumina had example RNA-Seq data we could look at. He gave me one link (fluentbio) and Karthik found another.

          https://www.fluentbio.com/species-mixture-experiment-with-large-cell-input/
          https://help.ica.illumina.com/project/p-cohorts/cohorts-publicdata

          Task: Find an example BAM file created using Illumina's single cell RNA-Seq pipeline and look to see if it has the CB/CR tags like the 10X genomics file.

            Attachments

              Issue Links

              relates to

              Task - A task that needs to be done. IGBF-3881 Add samtools filter by and color by options for CR and CB tags

              • Major - Major loss of function.
              • Closed

                Activity

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                nfreese Nowlan Freese created issue -
                nfreese Nowlan Freese made changes -
                Field Original Value New Value
                Epic Link IGBF-3765 [ 22984 ]
                karthik Karthik Raveendran made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Security Hidden [ 10001 ]
                karthik Karthik Raveendran made changes -
                Link This issue relates to IGBF-3881 [ IGBF-3881 ]
                karthik Karthik Raveendran made changes -
                Sprint Fall 1 [ 202 ]
                nfreese Nowlan Freese made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                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 -
                Sprint Fall 1, Fall 2 [ 202, 203 ] Fall 1 [ 202 ]
                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:
                    karthik Karthik Raveendran
                    Reporter:
                    nfreese Nowlan Freese
                  • Votes:
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                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: