# README.md

This **README** file provides a detailed description of the data files associated with the study titled ***"Metabolic reprogramming of protists within the microbiome of sinking particles"***.

## Files

1. **RepresentativeOEAGP_nucl.tar.gz**
– Description: Includes nucleotide sequences of the representative genes selected from the Oyashio Eukaryotic Active Gene Pools (OEAGP) used in this study.

2. **RepresentativeOEAGP_prot.tar.gz**
– Description: Includes amino acid sequences of the representative genes from the OEAGP used in this study.

3. **refseqgovemartrdrp.dmnd.tar.gz**
– Description: A custom taxonomy database incorporating sequences from MarFERReT, NCBI RefSeq, RNA viruses, and large DNA viruses from the GOEV dataset.

4. **TaxonomyDiamondHits.tar.gz**
– Description: Taxonomic annotations based on top 10% DIAMOND hits, refined using the lowest common ancestor method with NCBI taxonomy.

5. **all_T.emapper.annotations.tar.gz**
– Description: Functional annotations generated using eggNOG.

6. **KO_Orthology_ko00001.tsv**
- Description: This file contains gene funtion and pathway, and category information for every KO number.

## Directories:

1. **SALMONOUTPUT**
- Description: Directory containing quantification results of OEAGP sequences generated by Salmon. 
    - *numreads_oeagp*: Number of reads mapped to each sequence 
    - *tpm_oeagp*: Transcripts Per Million (TPM) values

2. **SpeciesLevelAnnotatedOutput**
- Description: Directory containing the recovered species-level taxonomic bins.
    - *EukTranMarFERReT_SpeciesLevelAnnotateOut*: This file contains the results of species-level annotation, where eukaryotic transcripts were selected and subjected to DIAMOND blastp against MarFERReT, with the best top hits used for annotation.
    - *taxid_XXX*: the recovered species-level "taxonomic bins".
    - *FilteredSampleOfBinsForDEGs.json*: This file contains the filtered samples for each species’ taxonomic bin used in the DEGs analysis.

3. **VirMakerCoreHMMProfile**
- Description: HMM profiles of viral marker and core genes used for virus detection.