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general:bioseqanalysis:genesetanalysis:fcat [2025/04/08 16:02] – [Preparing the fCAT run] ingogeneral:bioseqanalysis:genesetanalysis:fcat [2025/04/08 16:34] (current) – [fCAT analysis - Output visualization and interpretation] ingo
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 ==== fCAT analysis - Output visualization and interpretation ==== ==== fCAT analysis - Output visualization and interpretation ====
-fCAT in combination with [[https://bioconductor.org/packages/release/bioc/html/PhyloProfile.html|PhyloProfile]] allows to visualize and explore the results of the geneset completeness analysis. Follow the steps below to :!:  {{ :physaliacg:2024:data:eukaryota.tar.gz |download the data}} to your local computer and :!: to open it in PhyloProfile.+fCAT in combination with [[https://bioconductor.org/packages/release/bioc/html/PhyloProfile.html|PhyloProfile]] allows to visualize and explore the results of the geneset completeness analysis. Follow the steps below to :!:  {{ :physaliacg:2025:data:CRYPA_Metaeuk-fcat.tar.gz|download the data}} to your local computer and :!: to open it in PhyloProfile.
 <hidden PrecomputedFiles> <hidden PrecomputedFiles>
 You will find all pre-computed fCAT results at ''/home/ubuntu/Share/Analysis/fCAT/fcatOutput/eukaryota''. Use these, if your analysis did not complete in time. You will find all pre-computed fCAT results at ''/home/ubuntu/Share/Analysis/fCAT/fcatOutput/eukaryota''. Use these, if your analysis did not complete in time.
 </hidden> </hidden>
 === Downloading the data === === Downloading the data ===
-Download the following three files from the fcat output folder, e.g. ''$HOME/Analyses/fcat/fcatOutput/eukaryota/CRYHO@237895@220307/phyloprofileOutput'' for the //eukaryota// dataset.+Download the following three files from the fcat output folder, e.g. ''$HOME/Analyses/fcat/fcatOutput/eukaryota/CRYPA@5807@250408/phyloprofileOutput'' for the //eukaryota// dataset.
   - *.phyloprofile :!: These files contains the information about the presence/absence of orthologs to the genes in your coreset together with the domain architecture similarity scores. You will find the information for both your taxon of interest **and** the core taxa. **It is the main input file for PhyloProfile**. :!: Choose the one that is represents the fCAT scoring mode you are interested in.   - *.phyloprofile :!: These files contains the information about the presence/absence of orthologs to the genes in your coreset together with the domain architecture similarity scores. You will find the information for both your taxon of interest **and** the core taxa. **It is the main input file for PhyloProfile**. :!: Choose the one that is represents the fCAT scoring mode you are interested in.
   - *.mod.fa :!: This file contains the sequences of the orthologs in FASTA format   - *.mod.fa :!: This file contains the sequences of the orthologs in FASTA format
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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>