Output
======

.. _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:

.. code-block:: console

    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