meta data for this page
  •  

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
general:bioseqanalysis:genesetanalysis:taxaminer [2024/02/15 17:05] – [taXaminer analysis] ingogeneral:bioseqanalysis:genesetanalysis:taxaminer [2025/04/08 17:11] (current) – [taXaminer analysis] ingo
Line 20: Line 20:
   - 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/test_fritz/for_ingo/illumina_cryptov2.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]]. 
  
Line 33: Line 33:
   - 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>
Line 51: Line 51:
     * 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. We will be using ''/home/ubuntu/test_fritz/for_ingo/illumina_cryptov2.mapped.sort.bam''  +    * any read mapping information in BAM format  
-  - we will be using the unref50 database for the Diamond search. ''$HOME/Share/ProteinSets/uniref50/db.dmnd''+  - we will be using the unref50 database for the Diamond search. ''$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>
Line 62: Line 62:
 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: "$HOME/Share/ProteinSets/uniref50/db.dmnd"+database_path: "$HOME/Share/DBs/uniref50/db.dmnd"
  
 ############################################################# #############################################################
Line 87: Line 87:
 </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>