Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:3
-
Epic Link:
-
Sprint:Winter 1, Spring 1
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.
- Find one of Molly's recent deseq scripts to use as a template if not already having one.
- Pull each of the 4 gene counts tables.
- 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.