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  1. IGB
  2. IGBF-4052

Deseq2 on de novo salmon tables for all 4 tomato varieties

        Details

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

          GOAL: Given that we now have bam files and salmon count tables for each of the 4 tomato varieties, we can run Deseq2 on these tables and look at some relative comparisons within a variety.

          We can't compare across varieties. No common gene connections since this is de novo results.

          1. Find one of Molly's recent deseq scripts to use as a template if not already having one.
          2. Pull each of the 4 gene counts tables.
          3. Run each one and we can look at volcano plots, PCA, etc

          NEXTFLOW and Salmon produce many salmon count tables. I am guessing that this one:

          salmon.merged.gene_counts.tsv

          would be a good file to use. We don't TPM because deseq will take care of that.
          And we don't need transcript level.

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                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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                    Updated:
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