Commit 935aaebc authored by Celine Noirot's avatar Celine Noirot
Browse files

Adapt docs thanks to improvement

parent ce2ea34a
......@@ -132,13 +132,13 @@ The `results/` directory contains a sub-directory for each step launched:
| `SAMPLE_NAME/SAMPLE_NAME.pergene.tsv` | Taxonomic affiliation of genes. One line corresponds to a gene (1st column), its corresponding taxon id (2nd column), its corresponding lineage (3rd column) and the tax ids of each level of this lineage (4th column). |
| `SAMPLE_NAME/SAMPLE_NAME.warn.tsv` | List of genes with a hit without corresponding taxonomic affiliation. Each line corresponds to a gene (1st column), the reason why the gene is in this list (2nd column) and match ids into the database used during `05_alignment/05_2_database_alignment/` (3rd column). |
| `SAMPLE_NAME/SAMPLE_NAME.percontig.tsv` | Taxonomic affiliation of contigs. One line corresponds to a contig (1st column), its corresponding taxon id (2nd column), its corresponding lineage (3rd column) and the tax ids of each level of this lineage (4th column). |
| `SAMPLE_NAME/SAMPLE_NAME_quantif_percontig.tsv` | Quantification table of reads aligned on contigs affiliated to each lineage of the first column. One line = one taxonomic affiliation (1st column, `lineage_by_level`), the corresponding taxon id (2nd column, `consensus_tax_id`), the tax ids of each level of this taxonomic affiliation (3rd column, `tax_id_by_level`), the name of contigs affiliated to this lineage (4th column, `name_contigs`), the number of contigs affiliated to this lineage (5th column, `nb_contigs`) and the sum of the number of reads aligned to these contigs (6th column, `nb_reads`). |
| `SAMPLE_NAME/SAMPLE_NAME_quantif_percontig_by_[taxonomic_level].tsv` | One file by taxonomic level (superkingdom, phylum, order, class, family, genus, species) for the sample `SAMPLE_NAME`. Quantification table of reads aligned on contigs affiliated to each lineage of the corresponding [taxonomic level]. One line = one taxonomic affiliation at this [taxonomic level] with is taxon id (1st column, `tax_id_by_level`), its lineage (2nd column, `lineage_by_level`), the name of contigs affiliated to this lineage (3rd column, `name_contigs`), the number of contigs affiliated to this lineage (4th column, `nb_contigs`) and the sum of the number of reads aligned to these contigs (5th column, `nb_reads`). |
| `SAMPLE_NAME/SAMPLE_NAME_quantif_percontig.tsv` | Quantification table of reads aligned on contigs affiliated to each lineage of the first column. One line = one taxonomic affiliation (1st column, `lineage_by_level`), the corresponding taxon id (2nd column, `consensus_tax_id`), the tax ids of each level of this taxonomic affiliation (3rd column, `tax_id_by_level`), the name of contigs affiliated to this lineage (4th column, `name_contigs`), the number of contigs affiliated to this lineage (5th column, `nb_contigs`), the sum of the number of reads aligned to these contigs (6th column, `nb_reads`) and the mean depth of these contigs (6th column, `depth`). |
| `SAMPLE_NAME/SAMPLE_NAME_quantif_percontig_by_[taxonomic_level].tsv` | One file by taxonomic level (superkingdom, phylum, order, class, family, genus, species) for the sample `SAMPLE_NAME`. Quantification table of reads aligned on contigs affiliated to each lineage of the corresponding [taxonomic level]. One line = one taxonomic affiliation at this [taxonomic level] with is taxon id (1st column, `tax_id_by_level`), its lineage (2nd column, `lineage_by_level`), the name of contigs affiliated to this lineage (3rd column, `name_contigs`), the number of contigs affiliated to this lineage (4th column, `nb_contigs`), the sum of the number of reads aligned to these contigs (5th column, `nb_reads`) and the mean depth of these contigs (6th column, `depth`). |
| `SAMPLE_NAME/graphs/SAMPLE_NAME_aln_diamond.m8_contig_taxonomy_level.pdf` | Figure representing the number of contigs (y-axis) affiliated to each taxonomy levels (x-axis). |
| `SAMPLE_NAME/graphs/SAMPLE_NAME_aln_diamond.m8_prot_taxonomy_level.pdf` | Figure representing the number of proteins (y-axis) affiliated to each taxonomy levels (x-axis). |
| `SAMPLE_NAME/graphs/SAMPLE_NAME_aln_diamond.m8_nb_prot_annotated_and_assigned.pdf` | Figure representing the number of proteins (y-axis) in our contigs (`Total` bar), the number of proteins with a match into the database (`Annotated` bar) and the number of proteins with a match into the database which is found into the taxonomy (`Assigned` bar) (x-axis). |
| `quantification_by_contig_lineage_all.tsv` | Quantification table of reads aligned on contigs affiliated to each lineage. One line = one taxonomic affiliation with its lineage (1st column, `lineage_by_level`), the taxon id at each level of this lineage (2nd column, `tax_id_by_level`), and then all next 3-columns blocks correspond to one sample. Each 3-column block corresponds to the name of contigs affiliated to this lineage (1st column, `name_contigs_SAMPLE_NAME_quantif_percontig.tsv`), the number of contigs affiliated to this lineage (2nd column, `nb_contigs_SAMPLE_NAME_quantif_percontig.tsv`) and the sum of the number of reads aligned to these contigs (3rd column, `nb_reads_SAMPLE_NAME_quantif_percontig.tsv`). |
| `quantification_by_contig_lineage_[taxonomic_level].tsv` | One file by taxonomic level (superkingdom, phylum, order, class, family, genus, species). Quantification table of reads aligned on contigs affiliated to each lineage of the corresponding [taxonomic level]. One line = one taxonomic affiliation at this [taxonomic level] with its taxon id (1st column, `tax_id_by_level`), its lineage (2nd column, `lineage_by_level`), and then all next 3-columns blocks correspond to one sample. Each 3-column block corresponds to the name of contigs affiliated to this lineage (1st column, `name_contigs_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level].tsv`), the number of contigs affiliated to this lineage (2nd column, `nb_contigs_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level].tsv`) and the sum of the number of reads aligned to these contigs (3rd column, `nb_reads_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level].tsv`). |
| `quantification_by_contig_lineage_all.tsv` | Quantification table of reads aligned on contigs affiliated to each lineage. One line = one taxonomic affiliation with its lineage (1st column, `lineage_by_level`), the taxon id at each level of this lineage (2nd column, `tax_id_by_level`), and then all next 3-columns blocks correspond to one sample. Each 3-column block corresponds to the name of contigs affiliated to this lineage (1st column, `name_contigs_SAMPLE_NAME_quantif_percontig`), the number of contigs affiliated to this lineage (2nd column, `nb_contigs_SAMPLE_NAME_quantif_percontig`), the sum of the number of reads aligned to these contigs (3rd column, `nb_reads_SAMPLE_NAME_quantif_percontig`) and the mean depth of these contigs (4th column, `depth_SAMPLE_NAME_quantif_percontig`). |
| `quantification_by_contig_lineage_[taxonomic_level].tsv` | One file by taxonomic level (superkingdom, phylum, order, class, family, genus, species). Quantification table of reads aligned on contigs affiliated to each lineage of the corresponding [taxonomic level]. One line = one taxonomic affiliation at this [taxonomic level] with its taxon id (1st column, `tax_id_by_level`), its lineage (2nd column, `lineage_by_level`), and then all next 3-columns blocks correspond to one sample. Each 3-column block corresponds to the name of contigs affiliated to this lineage (1st column, `name_contigs_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level]`), the number of contigs affiliated to this lineage (2nd column, `nb_contigs_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level]`) and the sum of the number of reads aligned to these contigs (3rd column, `nb_reads_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level]`) and the mean depth of these contigs (4th column, `depth_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level]`). |
#### **08_binning/08_1_binning/**
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......@@ -1029,8 +1029,8 @@ In this directory you have results per sample of taxonomic affiliation of genes
#### 2. `07_taxo_affi/`
You can find in this directory two types of files:
- `quantification_by_contig_lineage_all.tsv`: the quantification table of reads aligned on contigs affiliated to each lineage. One line = one taxonomic affiliation with its lineage (1st column, `lineage_by_level`), the taxon id at each level of this lineage (2nd column, `tax_id_by_level`), and then all next 3-columns blocks correspond to one sample. Each 3-column block corresponds to the name of contigs affiliated to this lineage (1st column, `name_contigs_SAMPLE_NAME_quantif_percontig.tsv`), the number of contigs affiliated to this lineage (2nd column, `nb_contigs_SAMPLE_NAME_quantif_percontig.tsv`) and the sum of the number of reads aligned to these contigs (3rd column, `nb_reads_SAMPLE_NAME_quantif_percontig.tsv`). We cannot display this table here because even the first lines are too long.
- `quantification_by_contig_lineage_[taxonomic_level].tsv`: one file by taxonomic level (superkingdom, phylum, order, class, family, genus, species). Quantification table of reads aligned on contigs affiliated to each lineage of the corresponding [taxonomic level]. One line = one taxonomic affiliation at this [taxonomic level] with its taxon id (1st column, `tax_id_by_level`), its lineage (2nd column, `lineage_by_level`), and then all next 3-columns blocks correspond to one sample. Each 3-column block corresponds to the name of contigs affiliated to this lineage (1st column, `name_contigs_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level].tsv`), the number of contigs affiliated to this lineage (2nd column, `nb_contigs_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level].tsv`) and the sum of the number of reads aligned to these contigs (3rd column, `nb_reads_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level].tsv`).
- `quantification_by_contig_lineage_all.tsv`: the quantification table of reads aligned on contigs affiliated to each lineage. One line = one taxonomic affiliation with its lineage (1st column, `lineage_by_level`), the taxon id at each level of this lineage (2nd column, `tax_id_by_level`), and then all next 3-columns blocks correspond to one sample. Each 3-column block corresponds to the name of contigs affiliated to this lineage (1st column, `name_contigs_SAMPLE_NAME_quantif_percontig`), the number of contigs affiliated to this lineage (2nd column, `nb_contigs_SAMPLE_NAME_quantif_percontig`) and the sum of the number of reads aligned to these contigs (3rd column, `nb_reads_SAMPLE_NAME_quantif_percontig`) and the mean depth of these contigs (4th column, `depth_SAMPLE_NAME_quantif_percontig`). We cannot display this table here because even the first lines are too long.
- `quantification_by_contig_lineage_[taxonomic_level].tsv`: one file by taxonomic level (superkingdom, phylum, order, class, family, genus, species). Quantification table of reads aligned on contigs affiliated to each lineage of the corresponding [taxonomic level]. One line = one taxonomic affiliation at this [taxonomic level] with its taxon id (1st column, `tax_id_by_level`), its lineage (2nd column, `lineage_by_level`), and then all next 3-columns blocks correspond to one sample. Each 3-column block corresponds to the name of contigs affiliated to this lineage (1st column, `name_contigs_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level]`), the number of contigs affiliated to this lineage (2nd column, `nb_contigs_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level]`), the sum of the number of reads aligned to these contigs (3rd column, `nb_reads_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level]`) and the mean depth of these contigs (4th column, `depth_SAMPLE_NAME_quantif_percontig_by_[taxonomic_level]`).
The first lines if the table `quantification_by_contig_lineage_species.tsv` are:
```bash
......
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