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general:bioseqanalysis:genesetanalysis:taxaminer [2025/04/08 15:56] – [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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 gff_path: "AddYourInputDataHere" # path to GFF gff_path: "AddYourInputDataHere" # path to GFF
 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 hominis has the taxon id 237895+taxon_id: "AddYourInputDataHere" # NCBI Taxon ID of query species. Cryptosporidium parvum has the taxon id 5807
 database_path: "$HOME/Share/DBs/uniref50/db.dmnd" database_path: "$HOME/Share/DBs/uniref50/db.dmnd"