Output

The output files of Rp3 are organized in different subdirectories related to the mode that generated them. Look for the following tree-like structure:

outdir
├── counts  -- contains visualizations and counts table for ribocov mode
│   ├── plots       -- bar plots summarizing ribocov results
│   ├── raw
│   └── rpkm
├── databases
├── homology
│   ├── fasta_to_align
│   └── MSA
├── logs
├── metrics
├── multimappers
├── peptide_search
│   └── group
│       ├── gtf_name_target_database.fasta
│       └── gtf_name_target_decoy_database.fasta    -- .pin files generated by MSFragger.
├── phylogenetics   -- results from the annotate mode run with the flag --conservation. Formatted for visualization in Evolview.
│   └── blast       -- tblastn results for the identified smORFs
├── post_processing
│   └── group
│       └── db
├── rescore -- folder containing rescored results
│   ├── databases   -- rescored databases in .fasta format. These contain the microproteins from the first search + the provided proteome
│   ├── peptide_search      -- divided into subdirectories for each group. They contain the .pin files from MSFragger for the second round of searches
│   │   └── group
│   ├── post-processing             -- results from Percolator, divided into subdirectories for each group
│   │   └── group
│   └── summarized_results  -- folder containing the most important results
├── results
│   └── group
│       └── db
├── ribo-seq        -- folder containing results from the ribocov mode
│   ├── alignments  -- alignments in .sam format
│   ├── contaminant_alns    -- reads aligned to rRNAs or tRNAs (unused)
│   ├── sorted_bam_alignments       -- sorted alignments in .bam format
│   └── trimmed_reads       -- trimmed ribo-seq reads without adapters
├── spectra -- contains annotated spectra for each identified microprotein if the spectrum mode was run
│   └── annotated_spectra
├── summarized_results              -- main results before rescoring
│   ├── db
│   └── merged              -- merged results from every database (each gtf file generates a db)
└── translation             -- contains the 3 frame translation of the provided GTF files
    └── db