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general:bioseqanalysis:genesetanalysis [2022/03/07 11:04] – ingogeneral:bioseqanalysis:genesetanalysis [2024/02/15 06:58] (current) – ingo
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   - Assess the quality of the annotated gene set with respect to   - Assess the quality of the annotated gene set with respect to
-     - possibile contaminations. :!: We could have done this already during the assembly , e.g. using BlobTools, but we didn't… Think about whyCheck for contaminations. :!: We could have done this already during the assembly , e.g. using BlobTools, but we didn't… Think about why+     - possibile contaminations. :!: We could have done this already during the assembly , e.g. using [[https://blobtoolkit.genomehubs.org/blobtools2/|BlobTools]], but we didn't… 
     - completeness in terms of gene loci     - completeness in terms of gene loci
     - completeness of the gene structure     - completeness of the gene structure
-  - Trace evolutionary changes in the gene set. :!: We will be concentrating on the loss of genes in C. hominis. Think about why we have this focus.+  - Trace evolutionary changes in the gene set. :!: We will be concentrating on the loss of genes in //C. parvum//((why is analysing gene gain harder??))
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 Once you have completed this set of excersises, you should have an idea how to Once you have completed this set of excersises, you should have an idea how to
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   * [[:physaliacg|Main page of the Physalia course]]   * [[:physaliacg|Main page of the Physalia course]]
   * [[:physaliacg:genomeannotation|Previous work package: Genome annotation]]   * [[:physaliacg:genomeannotation|Previous work package: Genome annotation]]
-  * [[:general:bioseqanalysis:genesetanalysis:phyloprofile|Move to the next package: Phylogenetic profiles - fDOG]]+  * [[:physaliacg:genefunction|Move to the next package: Phylogenetic profiles - fDOG]]
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