From e2451161943c49c581db21f710ad7a1c5e8bd9fd Mon Sep 17 00:00:00 2001 From: "Josh L. Espinoza" Date: Thu, 22 Feb 2024 11:14:36 -0800 Subject: [PATCH] Update interpreting_module_outputs.md --- walkthroughs/docs/interpreting_module_outputs.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/walkthroughs/docs/interpreting_module_outputs.md b/walkthroughs/docs/interpreting_module_outputs.md index acb2bbb..473e303 100644 --- a/walkthroughs/docs/interpreting_module_outputs.md +++ b/walkthroughs/docs/interpreting_module_outputs.md @@ -231,6 +231,7 @@ ___________________________________________________________________ The main function of this module is classify viral genomes using `geNomad`. You can use either genomes recovered using `VEBA` or acquired elsewhere (e.g., NCBI, JGI, another tool). * **Taxonomy:** + * `taxonomy.tsv` - Viral genome classification based on `geNomad` * `taxonomy.clusters.tsv` - Viral cluster classification (If `--clusters` are provided) @@ -334,7 +335,7 @@ The main function of this module is map reads to `Bowtie2` index created by `ind To merge these counts tables together, run the following command from this [walkthrough](read_mapping_and_counts_tables.md): ```bash - # Merge contig-level counts (excu + # Merge contig-level counts merge_contig_mapping.py -m ${MAPPING_DIRECTORY} -c ${MAGS_TO_SLCS} -i ${SCAFFOLDS_TO_MAGS} -o ${OUT_DIR} # Merge ORF-level counts @@ -360,7 +361,6 @@ The main function of this module is estimate taxonomic abundances of a custom ge ```bash merge_generalized_mapping.py -o veba_output/profiling/taxonomy/merged.taxonomic_abundance.tsv.gz veba_output/profiling/taxonomy/*/output/taxonomic_abundance.tsv.gz - merge_generalized_mapping.py -o veba_output/profiling/taxonomy/merged.taxonomic_abundance.clusters.tsv.gz veba_output/profiling/taxonomy/*/output/taxonomic_abundance.clusters.tsv.gz ``` @@ -439,7 +439,7 @@ The main function of this module is run `antiSMASH`, reformat the results (tabul * **Visualization:** - * krona.html - HTML showing Krona plot for number of BGCs per protocluster-type. + * `krona.html` - HTML showing Krona plot for number of BGCs per protocluster-type. * **Prevalence tables:**