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general:bioseqanalysis:genesetanalysis:taxaminer [2024/02/09 14:53] – ingogeneral:bioseqanalysis:genesetanalysis:taxaminer [2025/04/08 17:11] (current) – [taXaminer analysis] ingo
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 **What you need** **What you need**
   - The genome sequence in fasta format. We will be using ''/home/ubuntu/Share/Assemblies/crypto_BCM2021_v2.fasta''   - The genome sequence in fasta format. We will be using ''/home/ubuntu/Share/Assemblies/crypto_BCM2021_v2.fasta''
-  - the annotation file in gff3. We will be using <code>/home/ubuntu/Share/Analysis/taxaminer/results/metaeuk</code>+  - the annotation file in gff3. We will be using <code>/home/ubuntu/Share/Analysis/taxaminer/results/metaeuk/Crypto_Metaeuk.sorted.gff3</code>
   - **optionally:** the protein fasta file. :!: taXaminer will extract the protein sequences from the gff file if not provided.   - **optionally:** the protein fasta file. :!: taXaminer will extract the protein sequences from the gff file if not provided.
-  - **optionally:** read mapping information: One BAM file per library+  - **optionally:** read mapping information: One BAM file per library ''/home/ubuntu/fritz/sv-detection/for_ingo/illumina_pairs.mapped.sort.bam'' 
 +  - **optionally** a local installation of the [[https://github.com/bionf/taxaminer-dashboard|taxaminer-dashboard]]. 
  
 **What you get** **What you get**
-  - a per-base coverage file. :!: Only when mapping information was provided +  - a taxonomic assignment for each gene based on a modified version of the DIAMOND Last Common Ancestor algorithm((We modified it a bit because we have a strong prior from which organism the gene should come from))
-  - a taxonomic assignment for each gene based on the DIAMOND Least Common Ancestor algorithm((in fact, we modified it a bit because we have a strong prior from which organism the gene should come from))+
   - a file with feature vectors for each gene in CSV   - a file with feature vectors for each gene in CSV
   - a html-file with the PCA as a 3D plotly plot   - a html-file with the PCA as a 3D plotly plot
 +  - a file with the proteins encoded by the annotated genes
 +  - a text file with the diamond hits 
  
 ==== Running taXaminer ==== ==== Running taXaminer ====
   - Check for the presence of taXaminer on your system. To do so:   - Check for the presence of taXaminer on your system. To do so:
     - activate the conda environment: <WRAP>     - activate the conda environment: <WRAP>
-<code>conda activate /home/ubuntu/anaconda3/envs/taxaminer</code>+<code>conda activate /home/ubuntu/miniconda3/envs/taxaminer</code>
 </WRAP> </WRAP>
     - issue the following command to test if you can run taxaminer: <WRAP>     - issue the following command to test if you can run taxaminer: <WRAP>
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     * The genome sequence in fasta file     * The genome sequence in fasta file
     * The genome annotation in gff3 format     * The genome annotation in gff3 format
-    * any read mapping information in BAM format+    * any read mapping information in BAM format  
 +  - we will be using the unref50 database for the Diamond search. ''$HOME/Share/DBs/uniref50/db.dmnd''
   - edit the config-script according to your needs<WRAP>   - edit the config-script according to your needs<WRAP>
 <hidden ConfigScriptExample> <hidden ConfigScriptExample>
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 output_path: "AddYourInputDataHere" # directory to save results to output_path: "AddYourInputDataHere" # directory to save results to
 taxon_id: "AddYourInputDataHere" # NCBI Taxon ID of query species. Cryptosporidium parvum has the taxon id 5807 taxon_id: "AddYourInputDataHere" # NCBI Taxon ID of query species. Cryptosporidium parvum has the taxon id 5807
 +database_path: "$HOME/Share/DBs/uniref50/db.dmnd"
  
 ############################################################# #############################################################
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 </hidden> </hidden>
 </WRAP> </WRAP>
-  - activate the taxaminer conda environment unless you have already done so((:!: It is a good idea to **deactivate** the environment that you are currently in)): <code>conda activate /home/ubuntu/anaconda3/envs/taxaminer</code> 
   - run taXaminer by issuing the following command((make sure that the correct conda environment is active))<WRAP><code>taxaminer.run config.yml</code>:!: Make sure that you are either in the directory where the config.yml is located, or provide the path.   - run taXaminer by issuing the following command((make sure that the correct conda environment is active))<WRAP><code>taxaminer.run config.yml</code>:!: Make sure that you are either in the directory where the config.yml is located, or provide the path.
 </WRAP> </WRAP>
-Once, the taXaminer run has completed, you can {{:physaliacg:2024:crypa_bcm2021-renamed_metaeuk.tar.gz |download the information}} to your local computer and open either the 3D_plot.html directly in a web browser. Alternatively, you can place the output folder into the //data// directory of the [[https://github.com/BIONF/taXaminer-dashboard|taXaminer-dashboard]]. +Once, the taXaminer run has completed, you can {{:physaliacg:2024:crypa_bcm2021-renamed_metaeuk.tar.gz |download the information}} to your local computer. Then you can either open the 3D_plot.html directly in a web browser, or you use the [[https://github.com/BIONF/taXaminer-dashboard|taXaminer-dashboard]] to first import the output folder and then load the data. 
  
   - :?: Are the results in line with your expectations   - :?: Are the results in line with your expectations