# subtract-index

## Usage:

crux subtract-index [options] <tide index 1> <tide index 2> <output index>

## Description:

This command takes two peptide indices, created by the tide-index command, and subtracts the second index from the first. The result is an output index that contains peptides that appear in the first index but not the second.

## Input:

• tide index 1 – A peptide index produced using tide-index
• tide index 2 – A second peptide index, to be subtracted from the first index.
• output index – A new peptide index containing all peptides that occur in thefirst index but not the second.

## 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:

• subtract-index.target.txt – a tab-delimited text file containing the target peptides.
• subtract-index.decoy.txt – a tab-delimited text file containing the decoy peptides.
• subtract-index.log.txt – a log file containing a copy of all messages that were printed to stderr.
• subtract-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.

## Options:

• ### Input and output

• --mass-precision <integer> – Set the precision for masses and m/z written to sqt and text files. Default = 4.
• --output-dir <string> – The name of the directory where output files will be created. Default = crux-output.
• --overwrite T|F – Replace existing files if true or fail when trying to overwrite a file if false. Default = false.
• --parameter-file <string> – A file containing parameters. See the parameter documentation page for details. Default = <empty>.
• --peptide-list T|F – Create in the output directory a text file listing of all the peptides in the database, along with their neutral masses, one per line. If decoys are generated, then a second file will be created containing the decoy peptides. Decoys that also appear in the target database are marked with an asterisk in a third column. Default = false.
• --verbosity <integer> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = 30.