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general:bioseqanalysis:genesetanalysis:taxaminer [2025/04/08 14:37] – [Running taXaminer] ingogeneral:bioseqanalysis:genesetanalysis:taxaminer [2025/04/08 17:11] (current) – [taXaminer analysis] ingo
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   - the annotation file in gff3. We will be using <code>/home/ubuntu/Share/Analysis/taxaminer/results/metaeuk/Crypto_Metaeuk.sorted.gff3</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 ''/home/ubuntu/fritz/sv-detection/short_reads/illumina_pairs.mapped.sort.bam''+  - **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]].    - **optionally** a local installation of the [[https://github.com/bionf/taxaminer-dashboard|taxaminer-dashboard]]. 
  
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-  - 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>