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  1. IGB
  2. IGBF-3863

Investigate Seurat marker gene alignments in IGB

        Details

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

          In IGBF-3838, the PBMC dataset of 2700 single cells was obtained and viewed in IGB. Almost all of the single cell RNA sequences for the genes (mentioned in the ticket) did not line up with the reference gene models. The reads are misaligned from the boundaries of the exons in the gene model. The UMI count matrix data for the PBMC dataset was used in the Seurat Guided Clustering Tutorial . To investigate further, view the the reads of the the marker genes mentioned in the tutorial in IGB and check how many are aligned with the gene model.

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              relates to

              Task - A task that needs to be done. IGBF-3864 Find more single cell RNA seq datasets in10XGenomics

              • Major - Major loss of function.
              • Closed

              Task - A task that needs to be done. IGBF-3838 Obtain and view sequence read alignments for PBMC dataset from Seurat vignette

              • Major - Major loss of function.
              • Closed

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