Commit 3b9d9340 authored by Joanna Fourquet's avatar Joanna Fourquet
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Update use_case.md

parent a406516a
......@@ -841,7 +841,7 @@ Into this directory you have 3 files associated to each sample named:
We are not going to describe this files here because they are intermediate files. For more explanations, see the [output documentation page](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/blob/dev/docs/output.md#06_func_annot06_3_functional_annotation).
There are 6 other files into this directory:
- `Quantifications_and_functional_annotations.tsv`: table where a row corresponds to an inter-sample cluster. Columns corresponds to quantification of aligned reads on each inter-sample cluster (columns *featureCounts.tsv), sum of abundance in all samples (column sum), eggNOG-mapper results (from seed_eggNOG_ortholog to PFAMs column) and diamond best hits results (last two columns diamond_db_idand diamond_db_description). The first lines of these file are:
- `Quantifications_and_functional_annotations.tsv`: table where a row corresponds to an inter-sample cluster. Columns corresponds to quantification of aligned reads on each inter-sample cluster (columns `*featureCounts.tsv`), sum of abundance in all samples (column `sum`), eggNOG-mapper results (from `seed_eggNOG_ortholog` to `PFAMs` column) and diamond best hits results (last two columns `diamond_db_id` and `diamond_db_description`). The first lines of these file are:
```bash
head Quantifications_and_functional_annotations.tsv
seed_cluster ERR3201914.featureCounts.tsv ERR3201918.featureCounts.tsv ERR3201928.featureCounts.tsv sum seed_eggNOG_ortholog seed_ortholog_evalue seed_ortholog_score eggNOG OGs narr_og_name narr_og_cat narr_og_desc best_og_name best_og_cat best_og_desc Preferred_name GOs EC KEGG_ko KEGG_Pathway KEGG_Module KEGG_Reaction KEGG_rclass BRITE KEGG_TC CAZy BiGG_Reaction PFAMs diamond_db_id diamond_db_description
......
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