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general:bioseqanalysis:genesetanalysis:fcat [2025/04/08 16:10] – [fCAT analysis - Output visualization and interpretation] ingogeneral:bioseqanalysis:genesetanalysis:fcat [2025/04/08 16:34] (current) – [fCAT analysis - Output visualization and interpretation] ingo
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   - upload the *domains file into the field at the lower left   - upload the *domains file into the field at the lower left
   - specify the origin of group IDs you are using   - specify the origin of group IDs you are using
-    - Dataset //alveolata//: select **OMA** 
     - Dataset //eukaryota//: select **OrthoDB**     - Dataset //eukaryota//: select **OrthoDB**
   - plot the results by clicking on ‘’Plot’’   - plot the results by clicking on ‘’Plot’’
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   - redo the selection, this time selecting all genes from the //eukaryota// dataset that are present in all core species but are absent in your //C. parvum// gene set((This requires some experimenting to find the correct clade in the tree, unfortunately))   - redo the selection, this time selecting all genes from the //eukaryota// dataset that are present in all core species but are absent in your //C. parvum// gene set((This requires some experimenting to find the correct clade in the tree, unfortunately))
   - if you do not find a single clade comprising all the genes that are missing in //C. parvum// do the following:   - if you do not find a single clade comprising all the genes that are missing in //C. parvum// do the following:
-    - Look for the file ''missing.txt'' in your fCat output folder+    - Look for the file ''{{ :physaliacg:2025:data:crypa_metaeuk-fcat_missing.txt.gz |missing.txt}}'' in your fCat output folder
     - go to the tab ''Customised profile''     - go to the tab ''Customised profile''
     - find the button to upload a gene list for selecting a gene set of interest<WRAP>     - find the button to upload a gene list for selecting a gene set of interest<WRAP>