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  1. IGB
  2. IGBF-3880

Investigate samtools tags consistency across datasets from Cell Ranger

        Details

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

          Description

          Single cell RNA seq data has samtools tags (see link below) and ultimately we want to filter reads in IGB using these tags especially CR or CB tags, which unique IDs for cells. But first we need to know if the tags are consistent across cellranger pipeline versions and a reliable filter. The datasets in IGBF-3864 should be good enough viewed and compared for samtools tags and confirm the consistency.
          https://samtools.github.io/hts-specs/SAMtags.pdf

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              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

              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-3864 Find more single cell RNA seq datasets in10XGenomics

              • Major - Major loss of function.
              • Closed

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                  • Assignee:
                    Unassigned
                    Reporter:
                    karthik Karthik Raveendran
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                    • Created:
                      Updated:
                      Resolved: