In this file tree overview of the annotation results, log files are ignored.
results/annotation/${sample}/
├── final_contigs.cmscan
├── final_contigs.faa
├── final_contigs.features.gff: Position of Open Reading Frames (ORFs), which were predicted by Prodigal.
├── final_contigs.ffn: Nucleotide sequences of ORFs.
├── final_contigs.gff
│
├── gene_counts.tsv: Counts of ORFs, also in other samples.
│
├── ${sample}.emapper.annotations: Predicted functional groups to which a query (in this case, an ORFs) correspond.
│ Fields include query (= predicted ORF), eggNOG_OGs, COG_category, GOs, multiple KEGG categories and Pfam.
├── ${sample}.emapper.seed_orthologs
├── ${sample}.pfam.out
├── infernal.log
│
│ The following glob patterns build filenames together:
├── enzymes.*
├── kos.*
├── modules.*
├── pathways.*
│ Files corresponding to these first four patterns are based upon the KEGG database.
│
├── pfam.*
│
├── *.parsed.tsv: Coupling of ORFs to KEGG database or protein families.
├── *.parsed.counts.tsv: Raw counts of KEGG entries or protein families.
│
│ Normalized counts, performed by edgeR:
├── *.parsed.TMM.tsv: edgeR's native normalization method
├── *.parsed.RLE.tsv: based upon DESeq
└── *.parsed.CSS.tsv: based upon metagenomeSeq