Custom - Summarize Taxonomic Counts Into Tsv Table ------------------------------------------------------ Take taxonomic counts and proportions from several samples and merge them together into a single table. Also calculate number of reads per sample for each taxonomic unit. **Location** - *Filepath:* /rules/paired_end/classification/report/taxonomic_counts/count_table/custom.snake - *Rule name:* custom__summarize_taxonomic_counts_into_tsv_table **Input(s):** - *krns:* Taxonomy files for each analysed sample in standardised format suitable for Krona graph generation **Output(s):** - *summary_xlsx:* Aggregated counts for each discovered taxonomy in Excel format - *summary_tsv:* Aggregated counts for each discovered taxonomy in tabular format - *subtax_xlsx:* Aggregated counts for each discovered taxonomy and its subtaxes in Excel format - *subtax_tsv:* Aggregated counts for each discovered taxonomy and its subtaxes in tabular format - *subtax_xlsx:* Normalised (counts for sample sum to 1) aggregated counts for each discovered taxonomy and its subtaxes in Excel format - *subtax_tsv:* Normalised (counts for sample sum to 1) aggregated counts for each discovered taxonomy and its subtaxes in tabular format Custom - Extract Taxonomic Level From Taxonomic Table --------------------------------------------------------- Extract read counts for organisms at selected taxonomic level, such as genus, species. **Location** - *Filepath:* /rules/paired_end/classification/report/taxonomic_counts/count_table/custom.snake - *Rule name:* custom__extract_taxonomic_level_from_taxonomic_table **Input(s):** - *subtax_tsv:* Aggregated counts for each discovered taxonomy and its subtaxes in tabular format **Output(s):** - *tax_level_abs:* Aggregated counts for single taxonomic level, e.g. species, order - *tax_level_rel:* Normalised (counts for a sample sum to 1) aggregated counts for single taxonomic level, e.g. species, order