# read-tide-index

## Usage:

`crux read-tide-index [options] <tide database>`

## Description:

Reads an index generated by tide-index and outputs information about the peptides it contains.

## Input:

- `tide database` – Either a FASTA file or a directory containing a database index created by a previous run of crux tide-index.

## Output:

The program writes files to the folder `crux-output` by default. The name of the output folder can be set by the user using the `--output-dir` option. The following files will be created:

- `read-tide-index.peptides.txt` – a tab-delimited file containing two columns with headers: the peptide, and a semicolon-delimited list of IDs of the proteins that peptide occurs in.
- `read-tide-index.params.txt` – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.
- `read-tide-index.log.txt` – a log file containing a copy of all messages that were printed to the screen during execution.

## Options:

- This command does not support any optional parameters.