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  1. IGB
  2. IGBF-3772

Run NEXTFLOW on contigs that are NOT SL4 or SL5

        Details

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

          GOAL:
          To set up and run an nf-core/rna-seq pipeline to align our RNA-Seq sequences against the de novo created contigs (Trinity, Spades).

          Next flow requires a GTF and a bed file along with the contigs. There are various ways to generate these and it is possible issues will arise from these files.

          Otherwise, we can follow Molly's protocol:
          https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit?usp=sharing

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              Task - A task that needs to be done. IGBF-3817 Create a method to compare NextFlow gene expression results

              • Major - Major loss of function.
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                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
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                    • Created:
                      Updated:
                      Resolved: