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general:bioseqanalysis:genesetanalysis:busco [2024/02/09 15:47] – ingogeneral:bioseqanalysis:genesetanalysis:busco [2024/02/14 14:24] (current) – [Busco Results] ingo
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 ===== Outline ===== ===== Outline =====
 **What you need** **What you need**
-  * The set of annotated proteins for your genome assembly((you can use any prediction)): ''/home/ubuntu/Share/Analysis/GeneAnnotation/Results/braker2/crypto_BCM2021_v2.braker2.proteins''+  * The set of annotated proteins for your genome assembly((you can use any prediction)): 
 +    * /home/ubuntu/Share/Analysis/GeneAnnotation/Results/braker2/crypto_BCM2021_v2.braker2.proteins 
 +    * /home/ubuntu/Share/Analysis/GeneAnnotation/Results/metaeuk/Crypto_Metaeuk.fas
   * **optionally** the genome assembly in FASTA format: ''/home/ubuntu/Share/Assemblies/crypto_BCM2021_v2.fasta''   * **optionally** the genome assembly in FASTA format: ''/home/ubuntu/Share/Assemblies/crypto_BCM2021_v2.fasta''
  
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 <code> <code>
 conda deactivate conda deactivate
-conda activate /home/ubuntu/miniconda3/envs/busco+conda activate busco
 busco -h busco -h
 </code> </code>
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 and check for the sets //alveolata// and //eukaryota// and check for the sets //alveolata// and //eukaryota//
   - run the Busco analysis by typing for example<WRAP>   - run the Busco analysis by typing for example<WRAP>
-<code>busco -i predsResults.fas -c 1 -o Busco_metaeuk_alveolata -m prot -l alveolata+<code>busco -i Crypto_Metaeuk.fas -c 1 -o Busco_metaeuk_eukaryota -m prot -l eukaryota
 </code> </code>
 </WRAP> </WRAP>
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 ===== Busco Results ===== ===== Busco Results =====
-  - Monitor the outcome of your analysis. <wrap hint></wrap>The output directory is quite nested. The interesting files are located for the //ubuntu user// in ''/home/ubuntu/Shared/busco/busco_crypto_alveolata/run_alveolata_odb10''  +  - Monitor the outcome of your analysis. <wrap hint></wrap>The output directory is quite nested. The interesting files are located for the //ubuntu user// in ''/home/ubuntu/Share/Analysis/busco/braker2/Busco_braker2_eukaryota/run_eukaryota_odb10/''
   - What do you conclude from the findings? Pay particular attention to the number of missing, partial and duplicated Busco genes, and **compare the results from the //eukaryota// and the //alveolata// data sets**.<WRAP>   - What do you conclude from the findings? Pay particular attention to the number of missing, partial and duplicated Busco genes, and **compare the results from the //eukaryota// and the //alveolata// data sets**.<WRAP>
 <hidden Spoiler> <hidden Spoiler>
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   - <wrap important></wrap>If you want to look up the orthologous group behind a BUSCO group, you have to look up at [[https://v10-1.orthodb.org/|OrthoDB]]((see the example in the hidden section above)). For looking up a gene in the assembly, check the fasta files in the directory ''fragmented_busco_sequences''. You will find the deviating gene from your assembly there. Use its identifier to search in the web browser.<WRAP>   - <wrap important></wrap>If you want to look up the orthologous group behind a BUSCO group, you have to look up at [[https://v10-1.orthodb.org/|OrthoDB]]((see the example in the hidden section above)). For looking up a gene in the assembly, check the fasta files in the directory ''fragmented_busco_sequences''. You will find the deviating gene from your assembly there. Use its identifier to search in the web browser.<WRAP>
-<hidden YouArePatient?> 
-8-) You are patient?? Good, then let's wait for the fCAT analysis 
-</hidden> 
 </WRAP> </WRAP>
   - **Optional** repeat the analysis with the genome sequence as input, but :?: do you think that this makes sense for our purpose? Keep also in mind that BUSCO search in an unannotated genome sequence is computationally more demanding than the search in protein sequences((Why?))   - **Optional** repeat the analysis with the genome sequence as input, but :?: do you think that this makes sense for our purpose? Keep also in mind that BUSCO search in an unannotated genome sequence is computationally more demanding than the search in protein sequences((Why?))