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  1. IGB
  2. IGBF-4340

Create python scripts to work with 10xGenomics files

        Details

        • Type: Task
        • Status: To-Do (View Workflow)
        • Priority: Major
        • Resolution: Unresolved
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          The goal of this task is to implement data preparation scripts that transform the input CSV file into a structure optimized for integration with IGB’s single-cell feature modules. Scripts such as:
          1) Color mapper for Loupe Browser barcode grouping files - Map Loupe browser cluster colors to the barcode grouping file
          2) HDF5 barcodes extractor

          These code for scripts will be is housed in https://bitbucket.org/KarthikRavee91/quickload_scrna-seq_10xgenomics/src/main/python_for_%20scRNA-seq/

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              relates to

              Task - A task that needs to be done. IGBF-4341 Create a scRNA-Seq tutorial

              • Major - Major loss of function.
              • Closed

                Activity

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                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 -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                karthik Karthik Raveendran made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
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                karthik Karthik Raveendran added a comment -

                Both scripts built and published in the downloads section of https://bitbucket.org/KarthikRavee91/quickload_scrna-seq_10xgenomics/downloads/

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                karthik Karthik Raveendran added a comment - Both scripts built and published in the downloads section of https://bitbucket.org/KarthikRavee91/quickload_scrna-seq_10xgenomics/downloads/
                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 ]
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                pkulzer Paige Kulzer (Inactive) added a comment -

                FYI the downloads section only contains Windows-compatible files, I can't run .exe on Mac. I will plan to run the python script from the repo instead!

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                pkulzer Paige Kulzer (Inactive) added a comment - FYI the downloads section only contains Windows-compatible files, I can't run .exe on Mac. I will plan to run the python script from the repo instead!
                pkulzer Paige Kulzer (Inactive) made changes -
                Link This issue relates to IGBF-4341 [ IGBF-4341 ]
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                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    karthik Karthik Raveendran
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                    Dates

                    • Created:
                      Updated: