IdentifySpuriousGeneSchema - Tutorial ===================================== Objective --------- This tutorial will guide you through the process of using the :doc:`IdentifySpuriousGene ` module to identify spurious genes in a schema. Prerequisites ------------- - Download the schema from `chewBBACA's tutorial `_. Procedure --------- 1. Open the terminal 2. Modify and run the following command to identify spurious genes in the schema: .. code-block:: bash SR IdentifySpuriousGenes -s '/path/to/tutorial_schema/schema_seed' -a '/path/to/Allele_calling' -o '/path/to/files/output_folder/IdentifySpuriousGenesSchema' -m schema -pm alleles_vs_alleles --t 11 -c 6 .. important:: Replace `/path/to/files/` with the actual path to the files. 1. Check the output directory for the list of identified spurious genes. The first lines of the file containing the clusters of potential spurious loci should look like this: :: Locus Action Class GCA-000730255-protein547 Join 1a GCA-000427055-protein583 Join 1a GCA-000730215-protein2131 Choice 4b GCA-000196055-protein1223 Choice 1c GCA-000007265-protein1233 Choice 1c GCA-000007265-protein534 Choice 1c GCA-000012705-protein1877 Choice 4b # GCA-000730215-protein1962 Join 1a GCA-000007265-protein1932 Join 1a GCA-000196055-protein485 Choice 1c GCA-000196055-protein1146 Choice 1c GCA-000196055-protein398 Choice 1c GCA-000427075-protein1286 Choice 1c # Example Output Structure ------------------------ To see the expected output structure, refer to the "Outputs" section in the :doc:`IdentifySpuriousGenes documentation `. Conclusion ---------- You have successfully identified spurious genes in a schema using the :doc:`IdentifySpuriousGene `.