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: <SnakeLines_dir>/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: <SnakeLines_dir>/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